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3D Structures of Biological Macromolecules
Part 1
Introduction: Facts, Tools and Fascination
Jürgen Sühnel
[email protected]
Institute of Molecular Biotechnology, Jena Centre for Bioinformatics
Jena / Germany
Supplementary Material: http://www.imb-jena.de/www_bioc/3D/
Biocomputing Group
Research
Identification and Analysis of Unusual Structural Motifs in
Proteins and Nucleic Acids
• C-H...O/N Interactions in RNA Structures
• Water-Mediated Base Pairs
• Base-Tetrad Motifs in DNA Mutiplex Structures
• C-H...-Interactions in Proteins
• Nest Motifs in Proteins (Non-repetitive Dipeptide Patterns)
Development of Tools for the Cost-effective Sequencing
of Microbial Genomes (Borrelia, Legionella, E. coli, Pseudomonas)
• GenColors
gencolors.imb-jena.de
Databases or Websites/Webtools for Molecular Biology
• The IMB Jena Image Library of Biological Macromolecules
• The RNA World Website
• The JCB Protein-Protein Interaction Website
• The Jena Prokaryotic Genome Viewer
• The Spirochetes Genome Browser
Service
Maintenance of the Institutional Computer Network
www.imb-jena.de/IMAGE.html
www.imb-jena.de/RNA.html
www.imb-jena.de/jcb/
jpgv.imb-jena.de
sgb.imb-jena.de
Different protein views
Structural Biology
Genomics
Porin
(1a0s)
Cell Biology
Systems Biology
SIR2p – NAD+-dependent histone deacetylase
PNC1 – pyrazinamidase/nicotinamidase 1)
Internal co-ordinates
(Bond) Distance
(Bond) Angle
Torsion angle
[2 atoms]
[3 atoms]
[4 atoms]
C
D
B
A
Protein structure
Sequence
Protein-protein or
protein-nucleic acid
complexes
Secondary structure
elements
Domains
Folds
Chains
Protein structure
The protein -helix
The first and still one of the greatest
triumphs of speculative model
building in structural
chemistry/biology
Forerunner of computer-assisted
model building
In the PNAS paper
the helix is drawn left-handed !!!!!
Linus Pauling and Robert Corey with a
wooden model of a protein -helix
(1 inch per Å)
Pauling, Corey, Branson.
The structure of proteins: Two hydrogen-bonded helical conformations of the polypeptide chain.
Proc. Natl. Acad. USA 1951, 37, 205-211.
Protein structure: domains
Protein structure: domains
Amino acids
Amino acids
Protein backbone torsion angles
D. W. Mount: Bioinformatics, Cold Spring Harbor Laboratory Press, 2001.
The Ramachandran map
Theoretical
Beta-sheet
Left-handed
alpha-helix
Right-handed
alpha-helix
Ramachandran, Ramakrishnan, Sasisekharan.
Stereochemistry and polypeptide chain configurations.
J. Mol. Biol. 1963, 7, 95-99.
Ramachandran, Sasisekheran.
Conformation of polypeptides and proteins.
Adv. Protein. Chem. 1968, 23, 283-438.
Experimental
237 384 amino acids in 1041 protein chains
Hovmöller et al., Acta Cryst. D 2002, 58, 768-776
non-glycines
glycines
Nucleic acid structure
History
History
History
Myoglobin model built by A. A. Barker, model maker in Cambridge (UK)
http://www.umass.edu/molvis/francoeur/barker/barker.html
Hemoglobin model
www2.mrc-lmb.cam.ac.uk/archive/Perutz62.html
Ideal B-DNA conformation
First single-crystal DNA structure (B-DNA)
Drew-Dickerson structure
H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R. E. Dickerson
Structure Of A B-/DNA Dodecamer. Conformation And Dynamics
Proc. Nat. Acad. Sci. Usa V. 78 2179 1981
The oldest myoglobin and hemoglobin structures in the PDB
Myoglobin (1mbn)
Hemoglobin (2dhb)
2 alpha chains: 146 aa (green, cyan)
2 beta chains: 141 aa (red, brown)
(Watsón, Kendrew: 1973)
(Perutz et al.: 1973)
The very first 3D biopolymer structures
The first three-dimensional structure of a biopolymer was the DNA model built by J. D. Watson and
F. H. C. Crick in 1953 taking into account fiber diffraction data provided by M. H. F. Wilkins and
others (Nobel Prize in Physiology or Medicine, 1962). The very first single-crystal DNA structure
was resolved by Dickerson and co-workers (PDB code: 1bna).
The first three-dimensional protein structures (myoglobin and hemoglobin) were determined by
M. F. Perutz and J. C. Kendrew (Nobel Prize in Chemistry, 1962).
The entries included in the PDB (PDB codes: 1mbn and 2dhb) represent refined structures.
J. C. Kendrew had obtained a myoglobin structure at a resolution of 6 Å already in 1957.
A. Klug has contributed substantially to the development of electron microscopy. This method is
suitable for systems that cannot be crystallized (Nobel Prize in Chemistry, 1982). A. Klug has applied
this method primarily to virus structures (see for example, Finch, Klug, J. Mol. Biol. 1965, 13, 1-12).
The structure of the first membrane-bound protein (a photosynthetic reaction centre; PDB code: 1prc)
was resolved by J. Deisenhofer, R. Huber and H. Michel (Nobel Prize in Chemistry, 1988).
The first three-dimensional protein structure determined by NMR spectroscopy was proteinase IIa
inhibitor from bull seminal plasma (PDB codes: 1bus, 2bus). It was reported by K. Wüthrich
and co-workers in 1985 (Nobel Prize in Chemistry, 2002).
Note, that in the early days of structural biology the PDB did not exist. It was created in 1970-1971.
Databases with 3D structural information
Comprehensive resources of biological macromolecules
Protein Data Bank (PDB)
PDBsum
Macromolecular Structure Data Base (MSD)
OCA
Jena Image Library of Biological Macromolecules
Nucleic-acid containing structures only
Nucleic Acid Database (NDB)
RNA Structure Database (RNAbase)
Protein structures only
Database of Comparative Protein Structure Models - ModBase
Structure-based classification of proteins
CATH
SCOP
Small molecules
National Cancer Institute 3D structure database (collection of 3D structures for over 400,000 drugs)
Cambridge Structural Database (CSD) (organic and metal-organic compounds including polypeptides
and polysaccharides up to 24 units)
For weblinks see: www.imb-jena.de/www_bioc/3D/
PDB file
HEADER
HYDROLASE (ENDORIBONUCLEASE)
12-MAY-95
1RTU
TITLE
USTILAGO SPHAEROGENA RIBONUCLEASE U2
COMPND
MOL_ID: 1;
COMPND
2 MOLECULE: RIBONUCLEASE U2;
COMPND
3 CHAIN: NULL
SOURCE
MOL_ID: 1;
SOURCE
2 ORGANISM_SCIENTIFIC: USTILAGO SPHAEROGENA;
SOURCE
3 ORGANISM_COMMON: SMUT FUNGUS;
SOURCE
4 ATCC: 12421
KEYWDS
HYDROLASE, ENDORIBONUCLEASE, BETA-ISOMERIZED ASPARTATE
EXPDTA
X-RAY DIFFRACTION
AUTHOR
S.NOGUCHI,Y.SATOW,T.UCHIDA,C.SASAKI,T.MATSUZAKI
REVDAT
1
08-NOV-96 1RTU
0
JRNL
AUTH
S.NOGUCHI,Y.SATOW,T.UCHIDA,C.SASAKI,T.MATSUZAKI
JRNL
TITL
CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA
JRNL
TITL 2 RIBONUCLEASE U2 AT 1.8 A RESOLUTION
JRNL
REF
BIOCHEMISTRY
V. 34 15583 1995
JRNL
REFN
ASTM BICHAW US ISSN 0006-2960
0033
REMARK
1
REMARK
2
REMARK
2 RESOLUTION. 1.80 ANGSTROMS.
REMARK
3
REMARK
3 REFINEMENT.
REMARK
3
PROGRAM
: PROLSQ
REMARK
3
AUTHORS
: KONNERT,HENDRICKSON
.
.
. SEQRES
1
114 CYS ASP ILE PRO GLN SER THR ASN CYS GLY GLY ASN VAL
SEQRES
2
114 TYR SER ASN ASP ASP ILE ASN THR ALA ILE GLN GLY ALA
SEQRES
3
114 LEU ASP ASP VAL ALA ASN GLY ASP ARG PRO ASP ASN TYR
SEQRES
4
114 PRO HIS GLN TYR TYR IAS GLU ALA SER GLU ASP ILE THR
SEQRES
5
114 LEU CYS CYS GLY SER GLY PRO TRP SER GLU PHE PRO LEU
SEQRES
6
114 VAL TYR ASN GLY PRO TYR TYR SER SER ARG ASP ASN TYR
SEQRES
7
114 VAL SER PRO GLY PRO ASP ARG VAL ILE TYR GLN THR ASN
SEQRES
8
114 THR GLY GLU PHE CYS ALA THR VAL THR HIS THR GLY ALA
SEQRES
9
114 ALA SER TYR ASP GLY PHE THR GLN CYS SER
MODRES 1RTU IAS
45 ASP BETA CARBOXY LINKED TO NEXT RESIDUE
.
ATOM
1 N
CYS
1
-4.933 19.344 18.255 1.00 5.83
ATOM
2 CA CYS
1
-6.309 19.098 17.823 1.00 7.72
ATOM
3 C
CYS
1
-6.270 18.283 16.532 1.00 8.17
ATOM
4 O
CYS
1
-5.179 17.995 16.022 1.00 8.08
ATOM
5 CB CYS
1
-7.128 20.382 17.691 1.00 6.94
ATOM
6 SG CYS
1
-6.599 21.528 16.386 1.00 8.61
ATOM
7 N
ASP
2
-7.451 17.930 16.012 1.00 9.26
.
N
C
C
O
C
S
N
Analysis and modeling tools
• Web-based tools
• Standalone programs
See compilation at
www.imb-jena.de/www_bioc/3D/
Cross references from other databases
IMB Jena Image Library of Biological Macromolecules (www.imb-jena.de/IMAGE.html)
RNABase
Systers
1 information request per minute
Reichert, Sühnel.
The IMB Jena Image Library of Biological Macromolecules
- 2002 update.
Nucleic Acids Res. 2002, 30, 253-254.
PDB content growth
2004:
~ 14 new structures per day
Image Library Start
PDB content statistics
 Total number of entries:
29874 (854)
 Entries listed by molecule type:
Proteins
Protein-nucleic acid complexes
Nucleic acids
Carbohydrates
27201 (756)
1242 (46)
1418 (52)
13 (0)
 Entries listed by method of structure determination:
Diffraction
NMR
Modeling
25474
4400
854
March 5, 2005
PDB extremes
 Entry with longest chain:
1ofd:
Glutamate synthase
[2 chains with 1491/1507 amino acids each;
each chain consists of 3 domains according to SCOP]
Glutamate synthases (GltS) are crucial enzymes in ammonia assimilation in plants
and bacteria, where they catalyze the formation of two molecules of L-glutamate from
L-glutamine and 2-oxoglutarate. The plant-type ferredoxin-dependent GltS and the
functionally homologous alpha subunit of the bacterial NADPH-dependent GltS are
complex four-domain monomeric enzymes of 140-165 kDa belonging to the
NH(2)-terminal nucleophile family of amidotransferases. The enzymes function through
the channeling of ammonia from the N-terminal amidotransferase domain to the
FMN-binding domain.
 Entries with largest number of chains:
1otz/1p0t
Baff-baff-R complex
[60 chains, two PDB files required]
B-cell activating factor (BAFF) is a key regulator of B-lymphocyte development.
Its biological role is mediated by the specific receptors BCMA, TACI and BAFF-R.
The cysteine-rich domain (CRD) of the BAFF-R extracellular domain adopts a
beta-hairpin structure and binds to the virus-like BAFF cage in a 1:1 molar ratio.
 Entry with largest number of models:
1e9t:
Human intestinal trefoil factor [NMR structure with 85 models]
Human intestinal trefoil factor, hITF, a secretory polypeptide found mainly in the
human gastrointestinal tract, is a member of the newly characterized trefoil factor or
P-domain peptide family representing putative growth factors.
PDB extremes: small peptide (peptaibol alamethicin, chain A, 1amt)
Three structural characteristics define the group of polypeptides
known as peptaibols:
A short chain length, typically between 15 and 20 residues,
although shorter ones are known.
A high proportion of the amino acid residues are non-standard.
There is a particular propensity for Aminoisobutyric acid (Aib).
The chain has an alkyl N terminus (usually acetyl) and a hydroxy-amino acid
at the C terminus.
Peptaibols generally exhibit antimicrobial activity and are referred to as
antibiotic peptides. The main sources of the peptaibols known to date are
fungii of the genre Trichoderma and Emericellopsis
The antomicrobial activity is thought to arise from the peptaibols'
membrane activity and their ability to form pores in lipid membranes.
The pores so formed are able to conduct ionic species; this conductance
leads to the loss of osmotic balance and cell death.
Along with Aib, non standard residues which have been observed include
Isovaline (Iva), Hydroxyproline (Hyp) and Ethylnorvaline (Etnor).
Aminoisobutyric acid has a high tendency to form helices and this is borne out
by the helical structures of the peptaibols.
www.cryst.bbk.ac.uk/peptaibol/introduction.htm
Quantitative helix bending analysis described in:
Kronen et al., J. Peptide Science 2003, 9, 729-724
Crystal structure and conformational analysis of ampullosporin A
Glutamate synthase (1ofd) – Jena Image Library atlas page
Glutamate synthase (1ofd) – Jena Image Library atlas page
Glutamate synthase (1ofd) – Jena Image Library atlas page: Jmol viewer
Glutamate synthase (1ofd) – Jena Image Library atlas page: Jmol viewer
Glutamate synthase (1ofd) – Jena Image Library atlas page
Glutamate synthase (1ofd) – Jena Image Library atlas page
Glutamate synthase (1ofd) – Jena Image Library atlas page: SCOP viewer
Glutamate synthase (1ofd) – Jena Image Library atlas page: Astex viewer
Glutamate synthase (1ofd) – Jena Image Library atlas page: WebMol viewer
Glutamate synthase (1ofd) – Jena Image Library atlas page: MolScript image
Glutamate synthase (1ofd) – Jena Image Library atlas page: Fe3S4 environment
Baff-Baff-R complex (1otz/1p0t)
This complex has 60 chains and therefore two PDB files are required for the complete structure,
Vision
www2.mrc-lmb.cam.ac.uk/groups/GS/eye.html
Rhodopsin (1f88) - 2000
Rhodopsin (1f88)
Microtubules
Cytoskeleton of a cultured epithelial cell.
Mircotubules are shown in green,
actin is shown in red and DNA is blue.
Image by Steve Rodgers.
3D Microtubule
image reconstruction
Microtubule model
sun.menloschool.org/~birchler/cells/animals/cytoskeleton/
www-vis.lbl.gov/Vignettes/KDowning-Microtubules/
users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Cytoskeleton.html
b-Tubulin dimer in complex with a taxol derivative (1tub) - 1997
The structure was solved by electron microscopy.
Ramachandran plots of the tubulin/taxol complex
Original structure at a resolution of 3.9 Å.
Refined structure at a resolution of 3.5 Å.
E. Nogales, S. G. Wolf, K. H. Downing
Structure Of The Alpha Beta Tubulin Dimer By Electron Crystallography
Nature V. 391 199 1998
J. Lowe, H. Li, K. H. Downing, E. Nogales
Refined Structure Of Alpha-Beta Tubulin At 3. 5 A Resolution
J. Mol. Biol. V. 313 1045 2001
Taxol (paclitaxel)
Pacific yew tree
Taxus brevifolia
A happy team of FSU Taxol researchers
led by Bob Holton (bottom row, right)
claimed victory in totally synthesizing the drug
on Dec. 9, 1993.
Hope in a Bottle:
Bristol-Myers Squibb introduced Taxol to the marketplace in January 1993.
From bark to business, the process took 31 years.
www.research.fsu.edu/researchr/fall2002/taxol.html
Cover images for all 2003/2004/2005 issues of the journal RNA
t-RNA (4tna) - 1978
Large ribosomal subunit (1jj2) - 2001
Nucleosome core particle (1aoi)
DNA in chromatin is organized in arrays
of nucleosomes.Two copies of each
histone protein, H2A, H2B, H3 and H4,
Are assembled into an octamer that has
145-147 base pairs of DNA wrapped
around it to form a nucleosome core.
Jena structures: 5S rRNA E-loop/L25 complex (1d6k)
IMB: Molecular Biophysics/NMR Spectroscopy (M. Görlach)
Jena structures: Macrophage infectivity potentiator protein (1fd9)
The human pathogen Legionella pneumophila,
the etiological agent of the severe and often fatal
Legionnaires' disease, produces a major virulence factor,
termed 'macrophage infectivity potentiator protein' (Mip),
that is necessary for optimal multiplication of the bacteria
within human alveolar macrophages.
Mip exhibits a peptidyl prolyl cis-trans isomerase (PPIase)
activity, which appears to be important for infection.
IMB: Structural Biology / Crystallography (R. Hilgenfeld)
Integration host factor (1ihf)
An architectural protein which assists formation of high order protein-DNA complexes such as
those found in replication and long distance transcription regulation.
Accelrys WebLab Viewer
See www.imb-jena.de/www_bioc/3D/ for availability
RasMol
See www.imb-jena.de/www_bioc/3D/ for availability
Program output of the program secstr (part of PROMOTIF)
PDB
numbering
Continous
numbering
phi
psi
secondary structure assignment
omega
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