8rve

Vimentin intermediate filament

Method: ELECTRON MICROSCOPY D_max: 290.2 Å Quality: GOOD

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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 × 78 PDB declaration: 78-meric（78） Consistent with protein copy count	Chain 0； UniProt 1–466 Chain 1； UniProt 1–466 Chain 2； UniProt 1–466 Chain 3； UniProt 1–466 Chain 4； UniProt 1–466 Chain 5； UniProt 1–466 Chain 6； UniProt 1–466 Chain 7； UniProt 1–466 Chain 8； UniProt 1–466 Chain 9； UniProt 1–466 Chain A； UniProt 1–466 Chain AA； UniProt 1–466 Chain AB； UniProt 1–466 Chain AC； UniProt 1–466 Chain AD； UniProt 1–466 Chain AE； UniProt 1–466 Chain AF； UniProt 1–466 Chain AG； UniProt 1–466 Chain AH； UniProt 1–466 Chain AI； UniProt 1–466 Chain AJ； UniProt 1–466 Chain AK； UniProt 1–466 Chain AL； UniProt 1–466 Chain AM； UniProt 1–466 Chain AN； UniProt 1–466 Chain AO； UniProt 1–466 Chain AP； UniProt 1–466 Chain B； UniProt 1–466 Chain C； UniProt 1–466 Chain D； UniProt 1–466 Chain E； UniProt 1–466 Chain F； UniProt 1–466 Chain G； UniProt 1–466 Chain H； UniProt 1–466 Chain I； UniProt 1–466 Chain J； UniProt 1–466 Chain K； UniProt 1–466 Chain L； UniProt 1–466 Chain M； UniProt 1–466 Chain N； UniProt 1–466 Chain O； UniProt 1–466 Chain P； UniProt 1–466 Chain Q； UniProt 1–466 Chain R； UniProt 1–466 Chain S； UniProt 1–466 Chain T； UniProt 1–466 Chain U； UniProt 1–466 Chain V； UniProt 1–466 Chain W； UniProt 1–466 Chain X； UniProt 1–466 Chain Y； UniProt 1–466 Chain Z； UniProt 1–466 Chain a； UniProt 1–466 Chain b； UniProt 1–466 Chain c； UniProt 1–466 Chain d； UniProt 1–466 Chain e； UniProt 1–466 Chain f； UniProt 1–466 Chain g； UniProt 1–466 Chain h； UniProt 1–466 Chain i； UniProt 1–466 Chain j； UniProt 1–466 Chain k； UniProt 1–466 Chain l； UniProt 1–466 Chain m； UniProt 1–466 Chain n； UniProt 1–466 Chain o； UniProt 1–466 Chain p； UniProt 1–466 Chain q； UniProt 1–466 Chain r； UniProt 1–466 Chain s； UniProt 1–466 Chain t； UniProt 1–466 Chain u； UniProt 1–466 Chain v； UniProt 1–466 Chain w； UniProt 1–466 Chain x； UniProt 1–466 Chain y； UniProt 1–466 Chain z； UniProt 1–466	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 7.20 Å

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 8RVE	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 method 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 experimental method 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 experimental method 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 experimental method 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 method 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 oligomeric state Different experimental method 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 method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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
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 method 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 method 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 method 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 0； PDBConstruct 1–466； UniProt 1–466 Author chain 1； PDBConstruct 1–466； UniProt 1–466 Author chain 2； PDBConstruct 1–466； UniProt 1–466 Author chain 3； PDBConstruct 1–466； UniProt 1–466 Author chain 4； PDBConstruct 1–466； UniProt 1–466 Author chain 5； PDBConstruct 1–466； UniProt 1–466 Author chain 6； PDBConstruct 1–466； UniProt 1–466 Author chain 7； PDBConstruct 1–466； UniProt 1–466 Author chain 8； PDBConstruct 1–466； UniProt 1–466 Author chain 9； PDBConstruct 1–466； UniProt 1–466 Author chain A； PDBConstruct 1–466； UniProt 1–466 Author chain AA； PDBConstruct 1–466； UniProt 1–466 Author chain AB； PDBConstruct 1–466； UniProt 1–466 Author chain AC； PDBConstruct 1–466； UniProt 1–466 Author chain AD； PDBConstruct 1–466； UniProt 1–466 Author chain AE； PDBConstruct 1–466； UniProt 1–466 Author chain AF； PDBConstruct 1–466； UniProt 1–466 Author chain AG； PDBConstruct 1–466； UniProt 1–466 Author chain AH； PDBConstruct 1–466； UniProt 1–466 Author chain AI； PDBConstruct 1–466； UniProt 1–466 Author chain AJ； PDBConstruct 1–466； UniProt 1–466 Author chain AK； PDBConstruct 1–466； UniProt 1–466 Author chain AL； PDBConstruct 1–466； UniProt 1–466 Author chain AM； PDBConstruct 1–466； UniProt 1–466 Author chain AN； PDBConstruct 1–466； UniProt 1–466 Author chain AO； PDBConstruct 1–466； UniProt 1–466 Author chain AP； PDBConstruct 1–466； UniProt 1–466 Author chain B； PDBConstruct 1–466； UniProt 1–466 Author chain C； PDBConstruct 1–466； UniProt 1–466 Author chain D； PDBConstruct 1–466； UniProt 1–466 Author chain E； PDBConstruct 1–466； UniProt 1–466 Author chain F； PDBConstruct 1–466； UniProt 1–466 Author chain G； PDBConstruct 1–466； UniProt 1–466 Author chain H； PDBConstruct 1–466； UniProt 1–466 Author chain I； PDBConstruct 1–466； UniProt 1–466 Author chain J； PDBConstruct 1–466； UniProt 1–466 Author chain K； PDBConstruct 1–466； UniProt 1–466 Author chain L； PDBConstruct 1–466； UniProt 1–466 Author chain M； PDBConstruct 1–466； UniProt 1–466 Author chain N； PDBConstruct 1–466； UniProt 1–466 Author chain O； PDBConstruct 1–466； UniProt 1–466 Author chain P； PDBConstruct 1–466； UniProt 1–466 Author chain Q； PDBConstruct 1–466； UniProt 1–466 Author chain R； PDBConstruct 1–466； UniProt 1–466 Author chain S； PDBConstruct 1–466； UniProt 1–466 Author chain T； PDBConstruct 1–466； UniProt 1–466 Author chain U； PDBConstruct 1–466； UniProt 1–466 Author chain V； PDBConstruct 1–466； UniProt 1–466 Author chain W； PDBConstruct 1–466； UniProt 1–466 Author chain X； PDBConstruct 1–466； UniProt 1–466 Author chain Y； PDBConstruct 1–466； UniProt 1–466 Author chain Z； PDBConstruct 1–466； UniProt 1–466 Author chain a； PDBConstruct 1–466； UniProt 1–466 Author chain b； PDBConstruct 1–466； UniProt 1–466 Author chain c； PDBConstruct 1–466； UniProt 1–466 Author chain d； PDBConstruct 1–466； UniProt 1–466 Author chain e； PDBConstruct 1–466； UniProt 1–466 Author chain f； PDBConstruct 1–466； UniProt 1–466 Author chain g； PDBConstruct 1–466； UniProt 1–466 Author chain h； PDBConstruct 1–466； UniProt 1–466 Author chain i； PDBConstruct 1–466； UniProt 1–466 Author chain j； PDBConstruct 1–466； UniProt 1–466 Author chain k； PDBConstruct 1–466； UniProt 1–466 Author chain l； PDBConstruct 1–466； UniProt 1–466 Author chain m； PDBConstruct 1–466； UniProt 1–466 Author chain n； PDBConstruct 1–466； UniProt 1–466 Author chain o； PDBConstruct 1–466； UniProt 1–466 Author chain p； PDBConstruct 1–466； UniProt 1–466 Author chain q； PDBConstruct 1–466； UniProt 1–466 Author chain r； PDBConstruct 1–466； UniProt 1–466 Author chain s； PDBConstruct 1–466； UniProt 1–466 Author chain t； PDBConstruct 1–466； UniProt 1–466 Author chain u； PDBConstruct 1–466； UniProt 1–466 Author chain v； PDBConstruct 1–466； UniProt 1–466 Author chain w； PDBConstruct 1–466； UniProt 1–466 Author chain x； PDBConstruct 1–466； UniProt 1–466 Author chain y； PDBConstruct 1–466； UniProt 1–466 Author chain z； PDBConstruct 1–466； UniProt 1–466

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	8rve
Deposition date deposition_date	2024-02-01
Structure title title	Vimentin intermediate filament
Keywords keywords	vimentin, intermediate filament, cytoskeleton, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	97.52 Å
Radius of gyration Rg (electron density) rg_electron	99.40 Å
Forward intensity I(0) i0	21520000000.00
Molecular weight molecular_weight	767860.0 kDa
Excluded volume excluded_volume	754630 Å³
Envelope volume envelope_volume	2220400 Å³
Hydration-shell volume shell_volume	211540 Å³
Envelope diameter envelope_diameter	333.2 Å
Shell Rg shell_rg	77.49 Å
Envelope Rg envelope_rg	94.17 Å
Shape Rg shape_rg	99.39 Å
Total Rg total_rg	99.22 Å
Total atoms total_atoms	54788
Residues n_residues	13697
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	290.2 Å
Rg (real space) rg_real	94.48 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	2.0840e+10
I(0) uncertainty (real space) i0_real_error	4.3970e+08
Rg (reciprocal space) rg_reciprocal	91.08 Å
I(0) (reciprocal space) i0_reciprocal	21070000000.0000
Solution quality estimate total_estimate	0.8710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	90.7 Å
Skewness Skewness skewness	0.566
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.7218
Highest regularization parameter α highest_alpha	21850000000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 0.967; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.045

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Resolution resolution	7.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	236920

Description description	Vimentin
Molecular weight formula_weight	53722.6 kDa
Source method src_method	man
Copy count entity_count	78

Polymer type type	polypeptide(L)
Chain IDs strand_id	;0,1,2,3,4,5,6,7,8,9,A,AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO,AP,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z ;
Atom count atom_count	54788

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

fit	/app/data/saxs_computation/rv/8rve/8rve.fit
pddf	/app/data/pr_computation/rv/8rve/8rve.pr.out
profile	/app/data/saxs_computation/rv/8rve/8rve.dat

Vimentin intermediate filament

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)