3c1v

The 1.5 A Crystal structure of Ca2+-bound S100A4

Method: X-RAY DIFFRACTION D_max: 81.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein S100-A4

Homo sapiens

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：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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–101 Chain D； UniProt 1–101	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

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 3C1V	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
3CGA Crystal structure of metastasis-associated protein S100A4 in the active, calcium-bound form Deposited 2008-03-05	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 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
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 34 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 13–113； UniProt 1–101 Author chain B； PDBConstruct 13–113； UniProt 1–101 Author chain C； PDBConstruct 13–113； UniProt 1–101 Author chain D； PDBConstruct 13–113； 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3c1v
Deposition date deposition_date	2008-01-24
Structure title title	The 1.5 A Crystal structure of Ca2+-bound S100A4
Keywords keywords	S100A4, Ca2+-bound, calcium-bound, CALCIUM BINDING PROTEIN; CALCIUM BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.99 Å
Radius of gyration Rg (electron density) rg_electron	24.21 Å
Forward intensity I(0) i0	32441000.00
Molecular weight molecular_weight	43951.0 kDa
Excluded volume excluded_volume	54902 Å³
Envelope volume envelope_volume	66841 Å³
Hydration-shell volume shell_volume	23325 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	30.77 Å
Envelope Rg envelope_rg	24.04 Å
Shape Rg shape_rg	24.22 Å
Total Rg total_rg	24.94 Å
Total atoms total_atoms	3061
Residues n_residues	380
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.0 Å
Rg (real space) rg_real	24.94 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	3.2440e+07
I(0) uncertainty (real space) i0_real_error	4.9270e+05
Rg (reciprocal space) rg_reciprocal	24.96 Å
I(0) (reciprocal space) i0_reciprocal	32440000.0000
Solution quality estimate total_estimate	0.8934
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.210
Kurtosis Kurtosis kurtosis	-0.504
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6207000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein S100-A4
Molecular weight formula_weight	13151.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3814

MRGSHHHHHHGSMACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRKK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	552

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3c1va_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

Domain ID domain_id	d3c1vb_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

Domain ID domain_id	d3c1vc_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

Domain ID domain_id	d3c1vd_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.2 — S100 proteins

CATH v4.4 (4 domains)

Domain ID domain_id	3c1vA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	3c1vB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	3c1vC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	3c1vD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	52.320 Å
Unit-cell length b length_b	52.320 Å
Unit-cell length c length_c	139.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	45.310 Å
R factor r_factor	0.1963
R_work r_work	0.1951
R_free r_free	0.2180

fit	/app/data/saxs_computation/c1/3c1v/3c1v.fit
pddf	/app/data/pr_computation/c1/3c1v/3c1v.pr.out
profile	/app/data/saxs_computation/c1/3c1v/3c1v.dat