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3cga

Crystal structure of metastasis-associated protein S100A4 in the active, calcium-bound form

Method: X-RAY DIFFRACTION Dmax: 58.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein S100-A4

Homo sapiens

UniProt P26447

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–101 Chain B； UniProt 1–101 Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；298 K；20% (w/v) PEG 3350 and 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50 Resolution 2.03 Å R-free 0.331

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3CGA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M31 Three-Dimensional Solution Structure of Apo-Mts1 Deposited 2002-06-26 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure ambient
NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 25mM；Pressure ambient
NMR sample composition 3mM Mts1, U-15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT | 93% H2O/7% D2O
NMR sample composition 3mM Mts1, U-13C,15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT | 93% H2O/7% D2O
Resolution not provided
2LNK Solution structure of Ca-bound S100A4 in complex with non-muscle myosin IIA Deposited 2011-12-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；313 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 0.5 mM protein_1, 1 mM [U-100% 13C; U-100% 15N] protein_2, 5 mM CALCIUM ION, 20 mM MES, 20 mM sodium chloride, 4 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MRD Solution structure of human Ca2+-loaded S100A4 cys-free mutant Deposited 2014-07-03 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Mutation：C3S,C76S,C81S,C86S Mutation：C3S,C76S,C81S,C86S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] S100A4-1, 16 mM TRIS-2, 8 mM sodium chloride-3, 6 mM calcium chloride-4, 0.1 mM EDTA-5, 0.34 mM sodium azide-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2Q91 Structure of the Ca2+-Bound Activated Form of the S100A4 Metastasis Factor Deposited 2007-06-12 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.05M ammonium sulfate, 0.05M Bis-Tris, 27.5% pentaethythritol-pthoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.63 Å R-free 0.217
3C1V The 1.5 A Crystal structure of Ca2+-bound S100A4 Deposited 2008-01-24 Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；40% PEG600, 0.1M CHES, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.50 Å R-free 0.218
3C1V The 1.5 A Crystal structure of Ca2+-bound S100A4 Deposited 2008-01-24 Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–101（101 aa）
Chain D 1–101（101 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；40% PEG600, 0.1M CHES, pH9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.50 Å R-free 0.218
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain S 1–101（101 aa）
Chain T 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–101（101 aa）
Chain D 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–101（101 aa）
Chain F 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1–101（101 aa）
Chain H 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 1–101（101 aa）
Chain J 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 1–101（101 aa）
Chain L 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 1–101（101 aa）
Chain N 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain O 1–101（101 aa）
Chain P 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3KO0 Structure of the tfp-ca2+-bound activated form of the s100a4 Metastasis factor Deposited 2009-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain Q 1–101（101 aa）
Chain R 1–101（101 aa）
Not recorded TFP 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M HEPES, 30% v/v Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.259
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 2–101（100 aa）
Chain B 2–101（100 aa）
Chain C 2–101（100 aa）
Chain D 2–101（100 aa）
Chain E 2–101（100 aa）
Chain F 2–101（100 aa）
Chain G 2–101（100 aa）
Chain H 2–101（100 aa）
Chain I 2–101（100 aa）
Chain J 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 12 CA CALCIUM ION × 20 DIO 1,4-DIETHYLENE DIOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–101（100 aa）
Chain B 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 3 CA CALCIUM ION × 4 DIO 1,4-DIETHYLENE DIOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 2–101（100 aa）
Chain D 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 2–101（100 aa）
Chain F 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 2–101（100 aa）
Chain H 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3M0W Structure of S100A4 with PCP Deposited 2010-03-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 2–101（100 aa）
Chain J 2–101（100 aa）
Not recorded P77 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine × 3 CA CALCIUM ION × 4 DIO 1,4-DIETHYLENE DIOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M Ammonium sulfate, 0.1M Tris pH 7.5, 20% PEG MME 5K, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.80 Å R-free 0.302
3ZWH Ca2+-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with myosin IIA Deposited 2011-07-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–101（101 aa）
Chain B 1–101（101 aa）
Mutation：YES Mutation：YES CA CALCIUM ION × 4 ACT ACETATE ION × 2 AZI AZIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；30% PEG 4000, 0.2 M NA-ACETATE PH 5.6, 0.1 M NA-CITRATE.
Resolution 1.94 Å R-free 0.206
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–88（88 aa） Fragment：RESIDUES 1-88
Chain D 1–88（88 aa） Fragment：RESIDUES 1-88
Mutation：YES Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500
Resolution 1.37 Å R-free 0.193
4CFQ Ca-bound truncated (delta13C) and C3S, C81S and C86S mutated S100A4 complexed with non-muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–88（88 aa） Fragment：RESIDUES 1-88
Chain B 1–88（88 aa） Fragment：RESIDUES 1-88
Mutation：YES Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.1 M MIB, PH 4, 25% W/V PEG 1500
Resolution 1.37 Å R-free 0.193
4CFR Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA Deposited 2013-11-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–101（101 aa） Fragment：RESDIUES 1-101
Chain B 1–101（101 aa） Fragment：RESDIUES 1-101
Mutation：YES Mutation：YES CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% W/V PEG 4000
Resolution 1.40 Å R-free 0.175
4ETO Structure of S100A4 in complex with non-muscle myosin-IIA peptide Deposited 2012-04-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–93（93 aa） Fragment：UNP residues 1-93
Chain B 1–93（93 aa） Fragment：UNP residues 1-93
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, 30% (v/v) Jeffamine ED-2001, Vapor diffusion, Sitting drop, temperature 298K
Resolution 1.54 Å R-free 0.251
4HSZ Structure of truncated (delta8C) S100A4 Deposited 2012-10-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–93（93 aa） Fragment：UNP residues 1-93
Chain B 1–93（93 aa） Fragment：UNP residues 1-93
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.25 Å R-free 0.277
4HSZ Structure of truncated (delta8C) S100A4 Deposited 2012-10-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–93（93 aa） Fragment：UNP residues 1-93
Chain D 1–93（93 aa） Fragment：UNP residues 1-93
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.0, Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.25 Å R-free 0.277
5LPU Crystal structure of Annexin A2 complexed with S100A4 Deposited 2016-08-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–101（101 aa）
Chain D 1–101（101 aa）
Not recorded CA CALCIUM ION × 14 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.1M Bis Tris pH 6.5, 0.2M ammonium acetate 4% PEG4000 and 1,5% glycerol
Resolution 2.10 Å R-free 0.207
6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–93（93 aa）
Chain A 2–93（92 aa）
Mutation：A280E,A280E,A280E,A280E Mutation：A280E,A280E,A280E,A280E GOL GLYCEROL × 2 CA CALCIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols 0.1 M Sodium HEPES; MOPS (acid) pH7.5 20% v/v Ethylene glycol; 10 % w/v PEG 8000 Morpheus D6
Resolution 3.10 Å R-free 0.272
6T58 Structure determination of the transactivation domain of p53 in complex with S100A4 using annexin A2 as a crystallization chaperone Deposited 2019-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–93（93 aa）
Chain B 2–93（92 aa）
Mutation：A280E,A280E,A280E,A280E Mutation：A280E,A280E,A280E,A280E GOL GLYCEROL × 2 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.12 M Alcohols 0.1 M Sodium HEPES; MOPS (acid) pH7.5 20% v/v Ethylene glycol; 10 % w/v PEG 8000 Morpheus D6
Resolution 3.10 Å R-free 0.272
7PSP Crystal structure of S100A4 labeled with NU000846b. Deposited 2021-09-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–100（100 aa）
Chain B 1–100（100 aa）
Not recorded 85Q (2R,4R)-1-(2-chloranylethanoyl)-N-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Labelled protein in 3M sodium chloride, 0.1M citrate, pH 3.5
Resolution 2.61 Å R-free 0.286
7PSQ Crystal structure of S100A4 labeled with NU074381b. Deposited 2021-09-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–100（100 aa）
Chain E 1–100（100 aa）
Not recorded CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 1 82Q (2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；MES 25mM, 12.5% ethylene glycol
Resolution 1.91 Å R-free 0.236
7PSQ Crystal structure of S100A4 labeled with NU074381b. Deposited 2021-09-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–100（100 aa）
Chain G 1–100（100 aa）
Not recorded CA CALCIUM ION × 5 EDO 1,2-ETHANEDIOL × 2 82Q (2~{R},4~{R})-1-ethanoyl-~{N}-naphthalen-1-yl-4-phenyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；MES 25mM, 12.5% ethylene glycol
Resolution 1.91 Å R-free 0.236

16 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S10A4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–101； UniProt 1–101 Author chain B； PDBConstruct 1–101； UniProt 1–101

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3cga

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cga
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cga
Deposition date deposition_date2008-03-05
Structure title titleCrystal structure of metastasis-associated protein S100A4 in the active, calcium-bound form
Keywords keywordscalcium-binding, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.34 Å
Radius of gyration Rg (electron density) rg_electron17.31 Å
Forward intensity I(0) i07510900.00
Molecular weight molecular_weight20343.0 kDa
Excluded volume excluded_volume25479 ų
Envelope volume envelope_volume29287 ų
Hydration-shell volume shell_volume14760 ų
Envelope diameter envelope_diameter59.2 Å
Shell Rg shell_rg22.47 Å
Envelope Rg envelope_rg17.46 Å
Shape Rg shape_rg17.32 Å
Total Rg total_rg18.11 Å
Total atoms total_atoms1416
Residues n_residues174
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.2 Å
Rg (real space) rg_real18.33 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real7.5110e+06
I(0) uncertainty (real space) i0_real_error8.6280e+04
Rg (reciprocal space) rg_reciprocal18.33 Å
I(0) (reciprocal space) i0_reciprocal7511000.0000
Solution quality estimate total_estimate0.6639
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.5 Å
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha852900.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cgaa_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins
Domain ID domain_idd3cgab_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.2 — S100 proteins

CATH v4.4 (2 domains)

Domain ID domain_id3cgaA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3cgaB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (1)

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9. Files and Curves (10)