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PDBsum entry 1hlu

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protein ligands metals Protein-protein interface(s) links
Complex (acetylation/actin-binding) PDB id
1hlu
Jmol
Contents
Protein chains
375 a.a.
140 a.a. *
Ligands
ATP
Metals
_CA
* Residue conservation analysis
PDB id:
1hlu
Name: Complex (acetylation/actin-binding)
Title: Structure of bovine beta-actin-profilin complex with actin bound atp phosphates solvent accessible
Structure: Beta-actin. Chain: a. Profilin. Chain: p
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: thymus. Organ: thymus
Biol. unit: Dimer (from PQS)
Resolution:
2.65Å     R-factor:   0.201     R-free:   0.330
Authors: J.K.Chik,U.Lindberg,C.E.Schutt
Key ref:
J.K.Chik et al. (1996). The structure of an open state of beta-actin at 2.65 A resolution. J Mol Biol, 263, 607-623. PubMed id: 8918942 DOI: 10.1006/jmbi.1996.0602
Date:
30-May-97     Release date:   15-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60712  (ACTB_BOVIN) -  Actin, cytoplasmic 1
Seq:
Struc:
375 a.a.
374 a.a.*
Protein chain
Pfam   ArchSchema ?
P02584  (PROF1_BOVIN) -  Profilin-1
Seq:
Struc:
140 a.a.
139 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   6 terms 
  Biological process     actin cytoskeleton organization   7 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1006/jmbi.1996.0602 J Mol Biol 263:607-623 (1996)
PubMed id: 8918942  
 
 
The structure of an open state of beta-actin at 2.65 A resolution.
J.K.Chik, U.Lindberg, C.E.Schutt.
 
  ABSTRACT  
 
The structure of an "open state" of crystalline profilin:beta-actin has been solved to 2.65 A by X-ray crystallography. The open-state crystals, in 1.8 M potassium phosphate, have an expanded unit cell dimension in the c direction of 185.7 A compared with 171.9 A in the previously solved ammonium sulphate-stabilized "tight-state" structure. The unit cell change between the open and the tight states is accompanied by large subdomain movements in actin. Furthermore, the nucleotide in the open state is significantly more exposed to solvent, and local conformational changes in the hydrophobic pocket surrounding cysteine 374 occur during the transition to the tight state. Significant changes were observed at the N terminus and in the DNase-I binding loop. Neither the structure of profilin nor its contact with beta-actin are affected by the changes in the unit cell. Applying osmotic pressure to profilin:beta-actin crystals brings about a collapse of the unit cell comparable with that seen in the open to tight-state transition, enabling an estimate of the work required to cause this transformation of beta-actin in the crystals. The slight difference in energy between the open and collapsed states explains the extreme sensitivity of profilin:beta-actin crystals to changes in chemical and thermal environment.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A stereo view of the C a trace of the open state of profilin:b-actin with ATP and Ca 2+ . The complex is oriented with the crystal b-axis vertical and the c-axis horizontal. Actin residues are numbered according to the a-actin convention (i.e. N-terminal residue is D2). Profilin (green) is numbered 1 to 139. The subdomains of actin as defined in the Figure are: 1 (cyan) residues 2 to 34, 70 to 145 and 334 to 375; 2 (red) 34 to 70; 3 (purple) 145 to 179, 272 to 334; 4 (orange) 179 to 272. All molecular representations were made in MOLSCRIPT (Kraulis, 1991).
Figure 10.
Figure 10. Stereoview of the ATP phosphate-binding site in the open and tight states of b-actin. The open and tight states of b-actin were aligned as in Figure 4. The main chain of the phosphate-binding loops N12--C17 and D154--H161 (carbonyl groups omitted) of open and tight states of b-actin are shown in cyan and black lines, respectively. The location of the Gly15 amide group is marked. The ATP is represented by balls and sticks (cyan, open state). O1B is green and O2B is red. The divalent cation is yellow. The labelling of the oxgen atoms follows that of the tight-state PDB file 2btf. In the DNase I:a-actin structure, the labelling of the oxygen atoms is reversed. The direction of view is approximately down the crystal b-axis.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 263, 607-623) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20718862 A.V.Pivovarova, S.Y.Khaitlina, and D.I.Levitsky (2010).
Specific cleavage of the DNase-I binding loop dramatically decreases the thermal stability of actin.
  FEBS J, 277, 3812-3822.  
20935633 V.E.Galkin, A.Orlova, G.F.Schröder, and E.H.Egelman (2010).
Structural polymorphism in F-actin.
  Nat Struct Mol Biol, 17, 1318-1323.  
19888216 Q.Zhong, N.Simonis, Q.R.Li, B.Charloteaux, F.Heuze, N.Klitgord, S.Tam, H.Yu, K.Venkatesan, D.Mou, V.Swearingen, M.A.Yildirim, H.Yan, A.Dricot, D.Szeto, C.Lin, T.Hao, C.Fan, S.Milstein, D.Dupuy, R.Brasseur, D.E.Hill, M.E.Cusick, and M.Vidal (2009).
Edgetic perturbation models of human inherited disorders.
  Mol Syst Biol, 5, 321.  
19289059 R.Kardos, K.Pozsonyi, E.Nevalainen, P.Lappalainen, M.Nyitrai, and G.Hild (2009).
The effects of ADF/cofilin and profilin on the conformation of the ATP-binding cleft of monomeric actin.
  Biophys J, 96, 2335-2343.  
19156817 T.Splettstoesser, F.Noé, T.Oda, and J.C.Smith (2009).
Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state.
  Proteins, 76, 353-364.  
19635839 W.A.Hofmann, A.Arduini, S.M.Nicol, C.J.Camacho, J.L.Lessard, F.V.Fuller-Pace, and P.de Lanerolle (2009).
SUMOylation of nuclear actin.
  J Cell Biol, 186, 193-200.  
18477565 B.M.Miller, and K.M.Trybus (2008).
Functional effects of nemaline myopathy mutations on human skeletal alpha-actin.
  J Biol Chem, 283, 19379-19388.  
18945676 E.Stokasimov, M.McKane, and P.A.Rubenstein (2008).
Role of intermonomer ionic bridges in the stabilization of the actin filament.
  J Biol Chem, 283, 34844-34854.  
18708324 G.M.Altschuler, and K.R.Willison (2008).
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin.
  J R Soc Interface, 5, 1391-1408.  
18316411 I.Rouiller, X.P.Xu, K.J.Amann, C.Egile, S.Nickell, D.Nicastro, R.Li, T.D.Pollard, N.Volkmann, and D.Hanein (2008).
The structural basis of actin filament branching by the Arp2/3 complex.
  J Cell Biol, 180, 887-895.  
18374941 K.B.Frederick, D.Sept, and E.M.De La Cruz (2008).
Effects of solution crowding on actin polymerization reveal the energetic basis for nucleotide-dependent filament stability.
  J Mol Biol, 378, 540-550.  
18689676 K.Baek, X.Liu, F.Ferron, S.Shu, E.D.Korn, and R.Dominguez (2008).
Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.
  Proc Natl Acad Sci U S A, 105, 11748-11753.
PDB codes: 3chw 3ci5 3cip
18223293 K.K.Wen, M.McKane, J.C.Houtman, and P.A.Rubenstein (2008).
Control of the ability of profilin to bind and facilitate nucleotide exchange from G-actin.
  J Biol Chem, 283, 9444-9453.  
17873883 A.Orlova, E.C.Garner, V.E.Galkin, J.Heuser, R.D.Mullins, and E.H.Egelman (2007).
The structure of bacterial ParM filaments.
  Nat Struct Mol Biol, 14, 921-926.
PDB code: 2qu4
  17650322 C.Butler-Cole, M.J.Wagner, M.Da Silva, G.D.Brown, R.D.Burke, and C.Upton (2007).
An ectromelia virus profilin homolog interacts with cellular tropomyosin and viral A-type inclusion protein.
  Virol J, 4, 76.  
17675344 D.Marushchak, S.Grenklo, T.Johansson, R.Karlsson, and L.B.Johansson (2007).
Fluorescence depolarization studies of filamentous actin analyzed with a genetic algorithm.
  Biophys J, 93, 3291-3299.  
17965017 E.Reisler, and E.H.Egelman (2007).
Actin structure and function: what we still do not understand.
  J Biol Chem, 282, 36133-36137.  
17914456 F.Ferron, G.Rebowski, S.H.Lee, and R.Dominguez (2007).
Structural basis for the recruitment of profilin-actin complexes during filament elongation by Ena/VASP.
  EMBO J, 26, 4597-4606.
PDB codes: 2pav 2pbd
17470807 J.K.Kamal, S.A.Benchaar, K.Takamoto, E.Reisler, and M.R.Chance (2007).
Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data.
  Proc Natl Acad Sci U S A, 104, 7910-7915.  
17599353 J.S.Allingham, C.O.Miles, and I.Rayment (2007).
A structural basis for regulation of actin polymerization by pectenotoxins.
  J Mol Biol, 371, 959-970.
PDB codes: 2q0r 2q0u
17526584 X.Zheng, K.Diraviyam, and D.Sept (2007).
Nucleotide effects on the structure and dynamics of actin.
  Biophys J, 93, 1277-1283.  
16757474 A.Pelikan Conchaudron, D.Didry, K.H.Le, E.Larquet, N.Boisset, D.Pantaloni, and M.F.Carlier (2006).
Analysis of tetramethylrhodamine-labeled actin polymerization and interaction with actin regulatory proteins.
  J Biol Chem, 281, 24036-24047.  
16920713 M.A.Rould, Q.Wan, P.B.Joel, S.Lowey, and K.M.Trybus (2006).
Crystal structures of expressed non-polymerizable monomeric actin in the ADP and ATP states.
  J Biol Chem, 281, 31909-31919.
PDB codes: 2hf3 2hf4
16882670 M.McKane, K.K.Wen, A.Meyer, and P.A.Rubenstein (2006).
Effect of the substitution of muscle actin-specific subdomain 1 and 2 residues in yeast actin on actin function.
  J Biol Chem, 281, 29916-29928.  
16672609 N.R.Buan, K.Rehfeld, and J.C.Escalante-Semerena (2006).
Studies of the CobA-type ATP:Co(I)rrinoid adenosyltransferase enzyme of Methanosarcina mazei strain Go1.
  J Bacteriol, 188, 3543-3550.  
16428279 T.J.Minehardt, P.A.Kollman, R.Cooke, and E.Pate (2006).
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
  Biophys J, 90, 2445-2449.  
15741975 A.H.Aguda, L.D.Burtnick, and R.C.Robinson (2005).
The state of the filament.
  EMBO Rep, 6, 220-226.  
16141336 D.S.Kudryashov, M.R.Sawaya, H.Adisetiyo, T.Norcross, G.Hegyi, E.Reisler, and T.O.Yeates (2005).
The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.
  Proc Natl Acad Sci U S A, 102, 13105-13110.
PDB code: 2a5x
15738427 J.L.Hodgkinson, C.Peters, S.A.Kuznetsov, and W.Steffen (2005).
Three-dimensional reconstruction of the dynactin complex by single-particle image analysis.
  Proc Natl Acad Sci U S A, 102, 3667-3672.  
15536092 K.E.Bryan, and P.A.Rubenstein (2005).
An intermediate form of ADP-F-actin.
  J Biol Chem, 280, 1696-1703.  
15505213 B.J.Nolen, R.S.Littlefield, and T.D.Pollard (2004).
Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP.
  Proc Natl Acad Sci U S A, 101, 15627-15632.
PDB codes: 1tyq 1u2v
15329672 E.Irobi, A.H.Aguda, M.Larsson, C.Guerin, H.L.Yin, L.D.Burtnick, L.Blanchoin, and R.C.Robinson (2004).
Structural basis of actin sequestration by thymosin-beta4: implications for WH2 proteins.
  EMBO J, 23, 3599-3608.
PDB code: 1t44
15163409 M.Hertzog, C.van Heijenoort, D.Didry, M.Gaudier, J.Coutant, B.Gigant, G.Didelot, T.Préat, M.Knossow, E.Guittet, and M.F.Carlier (2004).
The beta-thymosin/WH2 domain; structural basis for the switch from inhibition to promotion of actin assembly.
  Cell, 117, 611-623.
PDB code: 1sqk
14507709 D.S.Kudryashov, and E.Reisler (2003).
Solution properties of tetramethylrhodamine-modified G-actin.
  Biophys J, 85, 2466-2475.  
12923524 E.H.Egelman (2003).
A tale of two polymers: new insights into helical filaments.
  Nat Rev Mol Cell Biol, 4, 621-630.  
12356759 J.F.Dawson, E.P.Sablin, J.A.Spudich, and R.J.Fletterick (2003).
Structure of an F-actin trimer disrupted by gelsolin and implications for the mechanism of severing.
  J Biol Chem, 278, 1229-1238.
PDB code: 1mdu
12718516 M.A.Cusanovich, and T.E.Meyer (2003).
Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
  Biochemistry, 42, 4759-4770.  
12813032 P.Graceffa, and R.Dominguez (2003).
Crystal structure of monomeric actin in the ATP state. Structural basis of nucleotide-dependent actin dynamics.
  J Biol Chem, 278, 34172-34180.
PDB code: 1nwk
12732734 S.Vorobiev, B.Strokopytov, D.G.Drubin, C.Frieden, S.Ono, J.Condeelis, P.A.Rubenstein, and S.C.Almo (2003).
The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
  Proc Natl Acad Sci U S A, 100, 5760-5765.
PDB codes: 1d4x 1nlv 1nm1 1nmd 1yag
14578936 V.A.Klenchin, J.S.Allingham, R.King, J.Tanaka, G.Marriott, and I.Rayment (2003).
Trisoxazole macrolide toxins mimic the binding of actin-capping proteins to actin.
  Nat Struct Biol, 10, 1058-1063.
PDB codes: 1qz5 1qz6
14657234 V.E.Galkin, A.Orlova, M.S.VanLoock, A.Shvetsov, E.Reisler, and E.H.Egelman (2003).
ADF/cofilin use an intrinsic mode of F-actin instability to disrupt actin filaments.
  J Cell Biol, 163, 1057-1066.  
12167670 E.P.Sablin, J.F.Dawson, M.S.VanLoock, J.A.Spudich, E.H.Egelman, and R.J.Fletterick (2002).
How does ATP hydrolysis control actin's associations?
  Proc Natl Acad Sci U S A, 99, 10945-10947.  
12475943 G.Posern, A.Sotiropoulos, and R.Treisman (2002).
Mutant actins demonstrate a role for unpolymerized actin in control of transcription by serum response factor.
  Mol Biol Cell, 13, 4167-4178.  
12022877 H.J.Kinosian, L.A.Selden, L.C.Gershman, and J.E.Estes (2002).
Actin filament barbed end elongation with nonmuscle MgATP-actin and MgADP-actin in the presence of profilin.
  Biochemistry, 41, 6734-6743.  
12023237 I.V.Dedova, V.N.Dedov, N.J.Nosworthy, B.D.Hambly, and C.G.dos Remedios (2002).
Cofilin and DNase I affect the conformation of the small domain of actin.
  Biophys J, 82, 3134-3143.  
12191996 K.K.Wen, X.Yao, and P.A.Rubenstein (2002).
GTP-yeast actin.
  J Biol Chem, 277, 41101-41109.  
11932258 M.R.Bubb, L.Govindasamy, E.G.Yarmola, S.M.Vorobiev, S.C.Almo, T.Somasundaram, M.S.Chapman, M.Agbandje-McKenna, and R.McKenna (2002).
Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution.
  J Biol Chem, 277, 20999-21006.
PDB codes: 1ijj 1lcu
11882289 N.Lukoyanova, M.S.VanLoock, A.Orlova, V.E.Galkin, K.Wang, and E.H.Egelman (2002).
Each actin subunit has three nebulin binding sites: implications for steric blocking.
  Curr Biol, 12, 383-388.  
11751319 S.Y.Khaitlina, and H.Strzelecka-Gołaszewska (2002).
Role of the DNase-I-binding loop in dynamic properties of actin filament.
  Biophys J, 82, 321-334.  
11844798 T.Nyman, R.Page, C.E.Schutt, R.Karlsson, and U.Lindberg (2002).
A cross-linked profilin-actin heterodimer interferes with elongation at the fast-growing end of F-actin.
  J Biol Chem, 277, 15828-15833.  
11956227 V.E.Galkin, A.Orlova, M.S.VanLoock, I.N.Rybakova, J.M.Ervasti, and E.H.Egelman (2002).
The utrophin actin-binding domain binds F-actin in two different modes: implications for the spectrin superfamily of proteins.
  J Cell Biol, 157, 243-251.  
12211036 W.G.Krebs, V.Alexandrov, C.A.Wilson, N.Echols, H.Yu, and M.Gerstein (2002).
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
  Proteins, 48, 682-695.  
11940592 X.Yao, V.Nguyen, W.Wriggers, and P.A.Rubenstein (2002).
Regulation of yeast actin behavior by interaction of charged residues across the interdomain cleft.
  J Biol Chem, 277, 22875-22882.  
11524667 E.H.Egelman (2001).
Actin allostery again?
  Nat Struct Biol, 8, 735-736.  
11747839 E.H.Egelman (2001).
Molecular evolution: actin's long lost relative found.
  Curr Biol, 11, R1022-R1024.  
11737197 L.Blondin, V.Sapountzi, S.K.Maciver, C.Renoult, Y.Benyamin, and C.Roustan (2001).
The second ADF/cofilin actin-binding site exists in F-actin, the cofilin-G-actin complex, but not in G-actin.
  Eur J Biochem, 268, 6426-6434.  
10623728 E.Burke, N.M.Mahoney, S.C.Almo, and S.Barik (2000).
Profilin is required for optimal actin-dependent transcription of respiratory syncytial virus genome RNA.
  J Virol, 74, 669-675.  
10777749 E.M.De La Cruz, E.M.Ostap, R.A.Brundage, K.S.Reddy, H.L.Sweeney, and D.Safer (2000).
Thymosin-beta(4) changes the conformation and dynamics of actin monomers.
  Biophys J, 78, 2516-2527.  
10866806 H.Schüler, M.Nyåkern, C.E.Schutt, U.Lindberg, and R.Karlsson (2000).
Mutational analysis of arginine 177 in the nucleotide binding site of beta-actin.
  Eur J Biochem, 267, 4054-4062.  
10632717 H.Schüler, U.Lindberg, C.E.Schutt, and R.Karlsson (2000).
Thermal unfolding of G-actin monitored with the DNase I-inhibition assay stabilities of actin isoforms.
  Eur J Biochem, 267, 476-486.  
10878579 L.A.Boyer, and C.L.Peterson (2000).
Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?
  Bioessays, 22, 666-672.  
11031286 M.E.Wall, S.C.Gallagher, and J.Trewhella (2000).
Large-scale shape changes in proteins and macromolecular complexes.
  Annu Rev Phys Chem, 51, 355-380.  
10090737 C.E.Bystrom, D.W.Pettigrew, B.P.Branchaud, P.O'Brien, and S.J.Remington (1999).
Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.
  Biochemistry, 38, 3508-3518.
PDB codes: 1bwf 1glj 1gll
10491176 H.Schüler, E.Korenbaum, C.E.Schutt, U.Lindberg, and R.Karlsson (1999).
Mutational analysis of Ser14 and Asp157 in the nucleotide-binding site of beta-actin.
  Eur J Biochem, 265, 210-220.  
10037710 I.Gutsche-Perelroizen, J.Lepault, A.Ott, and M.F.Carlier (1999).
Filament assembly from profilin-actin.
  J Biol Chem, 274, 6234-6243.  
10388764 J.Moraczewska, B.Wawro, K.Seguro, and H.Strzelecka-Golaszewska (1999).
Divalent cation-, nucleotide-, and polymerization-dependent changes in the conformation of subdomain 2 of actin.
  Biophys J, 77, 373-385.  
9874766 L.D.Belmont, A.Orlova, D.G.Drubin, and E.H.Egelman (1999).
A change in actin conformation associated with filament instability after Pi release.
  Proc Natl Acad Sci U S A, 96, 29-34.  
10872464 M.A.Geeves, and K.C.Holmes (1999).
Structural mechanism of muscle contraction.
  Annu Rev Biochem, 68, 687-728.  
10354451 N.Fuller, and R.P.Rand (1999).
Water in actin polymerization.
  Biophys J, 76, 3261-3266.  
  9880332 V.Brault, U.Sauder, M.C.Reedy, U.Aebi, and C.A.Schoenenberger (1999).
Differential epitope tagging of actin in transformed Drosophila produces distinct effects on myofibril assembly and function of the indirect flight muscle.
  Mol Biol Cell, 10, 135-149.  
9631289 A.McGough (1998).
F-actin-binding proteins.
  Curr Opin Struct Biol, 8, 166-176.  
9789574 C.E.Schutt, and U.Lindberg (1998).
Muscle contraction as a Markov process. I: Energetics of the process.
  Acta Physiol Scand, 163, 307-323.  
9922146 E.Kim, E.Bobkova, C.J.Miller, A.Orlova, G.Hegyi, E.H.Egelman, A.Muhlrad, and E.Reisler (1998).
Intrastrand cross-linked actin between Gln-41 and Cys-374. III. Inhibition of motion and force generation with myosin.
  Biochemistry, 37, 17801-17809.  
9649308 E.Korenbaum, P.Nordberg, C.Björkegren-Sjögren, C.E.Schutt, U.Lindberg, and R.Karlsson (1998).
The role of profilin in actin polymerization and nucleotide exchange.
  Biochemistry, 37, 9274-9283.  
9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
  Nucleic Acids Res, 26, 4280-4290.  
9692980 V.K.Vinson, E.M.De La Cruz, H.N.Higgs, and T.D.Pollard (1998).
Interactions of Acanthamoeba profilin with actin and nucleotides bound to actin.
  Biochemistry, 37, 10871-10880.  
9545028 W.Wriggers, E.Mehler, F.Pitici, H.Weinstein, and K.Schulten (1998).
Structure and dynamics of calmodulin in solution.
  Biophys J, 74, 1622-1639.  
9484592 Y.A.Puius, N.M.Mahoney, and S.C.Almo (1998).
The modular structure of actin-regulatory proteins.
  Curr Opin Cell Biol, 10, 23-34.  
9153421 D.Safer, T.R.Sosnick, and M.Elzinga (1997).
Thymosin beta 4 binds actin in an extended conformation and contacts both the barbed and pointed ends.
  Biochemistry, 36, 5806-5816.  
9251782 W.Wriggers, and K.Schulten (1997).
Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop.
  Biophys J, 73, 624-639.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.