SAXSdb — 1gk7

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

VIMENTIN

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 101–137	Fragment：1A, RESIDUES 102-138	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；2.0M AMMONIUM ACETATE, 10%(V/V) DIOXANE, 0.1M MES/NA, PH6.5, pH 6.50	Resolution 1.40 Å R-free 0.216

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 1GK7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GK4 HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) Deposited 2001-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411 Chain B 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.17M NA ACETATE, 25.5% PEG8000, 0.1M CACODYLATE, PH6.5, pH 6.50	Resolution 2.30 Å R-free 0.262
1GK4 HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) Deposited 2001-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411 Chain D 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.17M NA ACETATE, 25.5% PEG8000, 0.1M CACODYLATE, PH6.5, pH 6.50	Resolution 2.30 Å R-free 0.262
1GK4 HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) Deposited 2001-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411 Chain F 327–410（84 aa） Fragment：CYS2, RESIDUES 328-411	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.17M NA ACETATE, 25.5% PEG8000, 0.1M CACODYLATE, PH6.5, pH 6.50	Resolution 2.30 Å R-free 0.262
1GK6 Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B) Deposited 2001-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 384–411（28 aa） Fragment：Z2B FUSION CONSTRUCT CONTAINING THE GCN4 LEUCINE ZIPPER LINKED TO VIMENTIN RESIDUES 385 - 412 Chain B 384–411（28 aa） Fragment：Z2B FUSION CONSTRUCT CONTAINING THE GCN4 LEUCINE ZIPPER LINKED TO VIMENTIN RESIDUES 385 - 412	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROPS WITH 12.5MG/ML PROTEIN AND 0.55M (NH4)2HPO4, PH ADJUSTED TO 9.0 WITH NAOH, AS PRECIPITANT	Resolution 1.90 Å R-free 0.227
3G1E X-ray crystal structure of coil 1A of human vimentin Deposited 2009-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 102–138（37 aa） Fragment：coil 1A Chain B 102–138（37 aa） Fragment：coil 1A	Mutation：Y117L Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Y117L Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；20 % PEG, 33 % isopropanol, 0.1 M trisodium citrate, pH 5.6, vapour diffusion, temperature 298K	Resolution 1.83 Å R-free 0.295
3KLT Crystal structure of a vimentin fragment Deposited 2009-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 263–334（72 aa） Fragment：UNP residues 263-334 Chain B 263–334（72 aa） Fragment：UNP residues 263-334 Chain C 263–334（72 aa） Fragment：UNP residues 263-334 Chain D 263–334（72 aa） Fragment：UNP residues 263-334	Not recorded	P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 SM SAMARIUM (III) ION × 3 P6G HEXAETHYLENE GLYCOL × 1 CA CALCIUM ION × 6 PG4 TETRAETHYLENE GLYCOL × 2 1PE PENTAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 27% PEG monoethylether 550, 27mM CaCl2, 7.5% (v/v) glycerol, 10mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.331
3KLT Crystal structure of a vimentin fragment Deposited 2009-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 263–334（72 aa） Fragment：UNP residues 263-334 Chain B 263–334（72 aa） Fragment：UNP residues 263-334	Not recorded	P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 SM SAMARIUM (III) ION × 2 P6G HEXAETHYLENE GLYCOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 27% PEG monoethylether 550, 27mM CaCl2, 7.5% (v/v) glycerol, 10mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.331
3KLT Crystal structure of a vimentin fragment Deposited 2009-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 263–334（72 aa） Fragment：UNP residues 263-334 Chain D 263–334（72 aa） Fragment：UNP residues 263-334	Not recorded	SM SAMARIUM (III) ION × 1 CA CALCIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 2 1PE PENTAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 27% PEG monoethylether 550, 27mM CaCl2, 7.5% (v/v) glycerol, 10mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.331
3S4R Crystal structure of vimentin coil1A/1B fragment with a stabilizing mutation Deposited 2011-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 99–189（91 aa） Fragment：coil 1A/1B fragment (UNP residues 99-189) Chain B 99–189（91 aa） Fragment：coil 1A/1B fragment (UNP residues 99-189)	Mutation：Y117L Mutation：Y117L	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M Na cacodylate, MPD 20%, Mg acetate 0.45M, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M MES, MPD 35%, 0.35M Li2SO4, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.315
3SSU Crystal structure of vimentin coil1A/1B fragment Deposited 2011-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 99–189（91 aa） Fragment：UNP residues 99-189 Chain B 99–189（91 aa） Fragment：UNP residues 99-189	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.04M calcium acetate, 0.1M MES pH 6, isopropanol 6%, VAPOR DIFFUSION, HANGING DROP, temperature 277K X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.06M calcium acetate, 0.1M MES pH 5.5, isopropanol 6%, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.272
3SWK Crystal structure of vimentin coil1B fragment Deposited 2011-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 153–238（86 aa） Fragment：coil 1B fragment (UNP residues 153-238) Chain B 153–238（86 aa） Fragment：coil 1B fragment (UNP residues 153-238)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；protein in 10 mM Tris pH 8, 38 mM NaCl + PEG 3350 25% w/v, 0.2M ammonium acetate, BIS-TRIS 0.1M pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.70 Å R-free 0.272
3TRT Crystal structure of stabilised vimentin coil2 fragment Deposited 2011-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 261–335（75 aa） Fragment：first half of vimentin coil2, UNP residues 261-335 Chain B 261–335（75 aa） Fragment：first half of vimentin coil2, UNP residues 261-335	Mutation：L265C, L269(MSE), C328(MSE) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L265C, L269(MSE), C328(MSE) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 GOL GLYCEROL × 3 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2M ammonium sulphate, 0.1M Tris pH8.5 + protein in 10 mM Tris pH 8, 38 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.298
3UF1 Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural Genomics Consortium Target HR4796B Deposited 2011-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 144–251（108 aa） Fragment：residues 144-255 Chain B 144–251（108 aa） Fragment：residues 144-255	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:NH4SO4 0.15M, TRISHCL 0.1M, PEG3350 18%, VAPOR DIFFUSION, HANGING DROP,	Resolution 2.81 Å R-free 0.284
3UF1 Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural Genomics Consortium Target HR4796B Deposited 2011-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 144–251（108 aa） Fragment：residues 144-255 Chain D 144–251（108 aa） Fragment：residues 144-255	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:NH4SO4 0.15M, TRISHCL 0.1M, PEG3350 18%, VAPOR DIFFUSION, HANGING DROP,	Resolution 2.81 Å R-free 0.284
4MCY Immune Receptor Deposited 2013-08-22	Different construct 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 C 66–78（13 aa） Fragment：UNP residues 66-78	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；26% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.30 Å R-free 0.225
4MCZ Immune Receptor Deposited 2013-08-22	Different construct 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 C 59–71（13 aa） Fragment：Residues 59-71	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；26% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.41 Å R-free 0.231
4MD0 Immune Receptor Deposited 2013-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 59–71（13 aa） Fragment：Residues 59-71	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；24% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.19 Å R-free 0.208
4MD5 Immune Receptor Deposited 2013-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 66–78（13 aa） Fragment：Residues 66-78	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 8 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；26% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.65 Å R-free 0.186
4MDI Immune Receptor Deposited 2013-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 66–78（13 aa） Fragment：Residues 66-78	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；25% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.203
4MDJ Immune Receptor Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 66–78（13 aa） Fragment：Residues 66-78	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；25% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.70 Å R-free 0.188
4YPC Trimeric crystal structure of vimentin coil1B fragment Deposited 2015-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: Trimeric	Chain A 161–243（83 aa） Fragment：coil 1B fragment, UNP residues 161-243	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；protein in 10 mM Tris pH 8, 38 mM NaCl mixed in ratio 1:1 with 1M Sodium citrate tribasic dihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5	Resolution 1.44 Å R-free 0.276
4YV3 Trimeric crystal structure of vimentin coil1B fragment Deposited 2015-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 161–238（78 aa） Chain B 161–238（78 aa） Chain C 161–238（78 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；10mg/ml protein in 10mM Tris-HCl pH 8, 38 mM NaCl mixed in v/v ratio 1:1 with ammonium sulphate 2.2M, sodium thiocyanate 0.2 M	Resolution 2.00 Å R-free 0.296
5WHF Crystal structure of vimentin coil 1B packed in a high-order filamentous form Deposited 2017-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 153–238（86 aa） Fragment：UNP residues 153-238 Chain B 153–238（86 aa） Fragment：UNP residues 153-238 Chain C 153–238（86 aa） Fragment：UNP residues 153-238 Chain D 153–238（86 aa） Fragment：UNP residues 153-238 Chain E 153–238（86 aa） Fragment：UNP residues 153-238 Chain F 153–238（86 aa） Fragment：UNP residues 153-238 Chain G 153–238（86 aa） Fragment：UNP residues 153-238 Chain H 153–238（86 aa） Fragment：UNP residues 153-238	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1 M Bis-Tris pH 6.5, 0.2 M magnesium acetate tetrahydrate and 10% PEG 8000	Resolution 2.25 Å R-free 0.282
6YXK Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74 Deposited 2020-05-03	Different construct 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 C 59–74（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20mM Tris pH 7.5, 20mM NaCl, 0.2M ammonium chloride pH 6.3, (20%) w/v PEG 3350)	Resolution 2.00 Å R-free 0.253
8RVE Vimentin intermediate filament Deposited 2024-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain 0 1–466（466 aa） Chain 1 1–466（466 aa） Chain 2 1–466（466 aa） Chain 3 1–466（466 aa） Chain 4 1–466（466 aa） Chain 5 1–466（466 aa） Chain 6 1–466（466 aa） Chain 7 1–466（466 aa） Chain 8 1–466（466 aa） Chain 9 1–466（466 aa） Chain A 1–466（466 aa） Chain AA 1–466（466 aa） Chain AB 1–466（466 aa） Chain AC 1–466（466 aa） Chain AD 1–466（466 aa） Chain AE 1–466（466 aa） Chain AF 1–466（466 aa） Chain AG 1–466（466 aa） Chain AH 1–466（466 aa） Chain AI 1–466（466 aa） Chain AJ 1–466（466 aa） Chain AK 1–466（466 aa） Chain AL 1–466（466 aa） Chain AM 1–466（466 aa） Chain AN 1–466（466 aa） Chain AO 1–466（466 aa） Chain AP 1–466（466 aa） Chain B 1–466（466 aa） Chain C 1–466（466 aa） Chain D 1–466（466 aa） Chain E 1–466（466 aa） Chain F 1–466（466 aa） Chain G 1–466（466 aa） Chain H 1–466（466 aa） Chain I 1–466（466 aa） Chain J 1–466（466 aa） Chain K 1–466（466 aa） Chain L 1–466（466 aa） Chain M 1–466（466 aa） Chain N 1–466（466 aa） Chain O 1–466（466 aa） Chain P 1–466（466 aa） Chain Q 1–466（466 aa） Chain R 1–466（466 aa） Chain S 1–466（466 aa） Chain T 1–466（466 aa） Chain U 1–466（466 aa） Chain V 1–466（466 aa） Chain W 1–466（466 aa） Chain X 1–466（466 aa） Chain Y 1–466（466 aa） Chain Z 1–466（466 aa） Chain a 1–466（466 aa） Chain b 1–466（466 aa） Chain c 1–466（466 aa） Chain d 1–466（466 aa） Chain e 1–466（466 aa） Chain f 1–466（466 aa） Chain g 1–466（466 aa） Chain h 1–466（466 aa） Chain i 1–466（466 aa） Chain j 1–466（466 aa） Chain k 1–466（466 aa） Chain l 1–466（466 aa） Chain m 1–466（466 aa） Chain n 1–466（466 aa） Chain o 1–466（466 aa） Chain p 1–466（466 aa） Chain q 1–466（466 aa） Chain r 1–466（466 aa） Chain s 1–466（466 aa） Chain t 1–466（466 aa） Chain u 1–466（466 aa） Chain v 1–466（466 aa） Chain w 1–466（466 aa） Chain x 1–466（466 aa） Chain y 1–466（466 aa） Chain z 1–466（466 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
8TRQ T cell recognition of citrullinated vimentin peptide presented by HLA-DR4 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 59–71（13 aa） Fragment：UNP residues 59-71 with modified residue citrulline (CIR) at position 64	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% w/v PEG3350, 0.2 M di-sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, tri-glycine additive	Resolution 2.75 Å R-free 0.264
8TRR T cell recognition of citrullinated vimentin peptide presented by HLA-DR4 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 59–71（13 aa） Fragment：UNP residues 59-71 with modified residue citrulline (CIR) at position 64	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 7 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% w/v PEG8000, 0.1 M Tris, pH 8.5, 0.2 M ammonium sulfate	Resolution 2.65 Å R-free 0.244
8TRR T cell recognition of citrullinated vimentin peptide presented by HLA-DR4 Deposited 2023-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 59–71（13 aa） Fragment：UNP residues 59-71 with modified residue citrulline (CIR) at position 64	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3 SO4 SULFATE ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% w/v PEG8000, 0.1 M Tris, pH 8.5, 0.2 M ammonium sulfate	Resolution 2.65 Å R-free 0.244

22 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VIME_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–39； UniProt 101–137

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gk7
Deposition date deposition_date	2001-08-08
Structure title title	HUMAN VIMENTIN COIL 1A FRAGMENT (1A)
Keywords keywords	VIMENTIN, INTERMEDIATE FILAMENT, HEPTAD REPEAT; VIMENTIN
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	17.20 Å
Radius of gyration Rg (electron density) rg_electron	17.16 Å
Forward intensity I(0) i0	565348.00
Molecular weight molecular_weight	4742.0 kDa
Excluded volume excluded_volume	5884 Å³
Envelope volume envelope_volume	7788 Å³
Hydration-shell volume shell_volume	5269 Å³
Envelope diameter envelope_diameter	63.8 Å
Shell Rg shell_rg	18.23 Å
Envelope Rg envelope_rg	17.76 Å
Shape Rg shape_rg	17.03 Å
Total Rg total_rg	17.75 Å
Total atoms total_atoms	333
Residues n_residues	39
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	66.8 Å
Rg (real space) rg_real	17.76 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	5.6530e+05
I(0) uncertainty (real space) i0_real_error	7.6490e+03
Rg (reciprocal space) rg_reciprocal	17.69 Å
I(0) (reciprocal space) i0_reciprocal	565300.0000
Solution quality estimate total_estimate	0.6629
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.6 Å
Skewness Skewness skewness	0.704
Kurtosis Kurtosis kurtosis	-0.211
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31080.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.216; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.009; Smooth: 0.957

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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	VIMENTIN
Molecular weight formula_weight	4654.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	375

GSNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1gk7a_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
Family Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

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8. Citations (2)

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Unit-cell length a length_a	56.770 Å
Unit-cell length b length_b	56.770 Å
Unit-cell length c length_c	58.420 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 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.1980
R_work r_work	0.1970
R_free r_free	0.2160

fit	/app/data/saxs_computation/gk/1gk7/1gk7.fit
pddf	/app/data/pr_computation/gk/1gk7/1gk7.pr.out
profile	/app/data/saxs_computation/gk/1gk7/1gk7.dat

HUMAN VIMENTIN COIL 1A FRAGMENT (1A)

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

VIMENTIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction