SAXSdb — 3swk

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 153–238 Chain B； UniProt 153–238	Fragment：coil 1B fragment (UNP residues 153-238)	No other associated polymer	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

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 3SWK	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 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 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 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 oligomeric state 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
1GK7 HUMAN VIMENTIN COIL 1A FRAGMENT (1A) 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 monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–137（37 aa） Fragment：1A, RESIDUES 102-138	Not recorded	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
3G1E X-ray crystal structure of coil 1A of human vimentin Deposited 2009-01-29	Different construct Different mutation/modification 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 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 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 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 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
3TRT Crystal structure of stabilised vimentin coil2 fragment Deposited 2011-09-10	Different construct Different mutation/modification 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 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 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 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	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 mutation/modification Different oligomeric state 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 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 1–86； UniProt 153–238 Author chain B； PDBConstruct 1–86； UniProt 153–238

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	3swk
Deposition date deposition_date	2011-07-14
Structure title title	Crystal structure of vimentin coil1B fragment
Keywords keywords	cytoskeleton, intermediate filament, alpha-helix, STRUCTURAL PROTEIN; STRUCTURAL 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	34.68 Å
Radius of gyration Rg (electron density) rg_electron	37.32 Å
Forward intensity I(0) i0	8199710.00
Molecular weight molecular_weight	20578.0 kDa
Excluded volume excluded_volume	25259 Å³
Envelope volume envelope_volume	38319 Å³
Hydration-shell volume shell_volume	11900 Å³
Envelope diameter envelope_diameter	137.8 Å
Shell Rg shell_rg	30.49 Å
Envelope Rg envelope_rg	38.71 Å
Shape Rg shape_rg	37.30 Å
Total Rg total_rg	36.75 Å
Total atoms total_atoms	1441
Residues n_residues	171
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	130.9 Å
Rg (real space) rg_real	36.41 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	8.2440e+06
I(0) uncertainty (real space) i0_real_error	1.3240e+05
Rg (reciprocal space) rg_reciprocal	35.08 Å
I(0) (reciprocal space) i0_reciprocal	8195000.0000
Solution quality estimate total_estimate	0.4308
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	0.693
Kurtosis Kurtosis kurtosis	-0.323
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	2.1310
Highest regularization parameter α highest_alpha	279100.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.105; Stabil: 0.963; Sysdev: 0.000; Positv: 1.000; Valcen: 0.017; Smooth: 0.383

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3swkA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1160 — Vasodilator-stimulated phosphoprotein

Domain ID domain_id	3swkB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1160 — Vasodilator-stimulated phosphoprotein

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8. Citations (1)

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Unit-cell length a length_a	40.150 Å
Unit-cell length b length_b	54.460 Å
Unit-cell length c length_c	44.090 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	34.299 Å
R factor r_factor	0.2335
R_work r_work	0.2315
R_free r_free	0.2723

Description description	Vimentin
Molecular weight formula_weight	10397.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1694

Crystal structure of vimentin coil1B fragment

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

fit	/app/data/saxs_computation/sw/3swk/3swk.fit
pddf	/app/data/pr_computation/sw/3swk/3swk.pr.out
profile	/app/data/saxs_computation/sw/3swk/3swk.dat