SAXSdb — 4u7y

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

Vacuolar protein sorting-associated protein 4B

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–89	Fragment：MIT domain (UNP residues 1-89)	IST1 homolog × 1 （P53990）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.3；299 K；2.58 M Na-malonate	Resolution 2.50 Å R-free 0.271

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 4U7Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WR0 Structural characterization of the MIT domain from human Vps4b Deposited 2004-10-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–77（77 aa） Fragment：MIT DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) NaCl 50mM；Pressure 1 NMR sample composition 1mM protein U-15N; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT \| 95% H2O/5% D2O NMR sample composition 1mM protein U-15N,13C; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT \| 95% H2O/5% D2O	Resolution not provided
1XWI Crystal Structure of VPS4B Deposited 2004-11-01	Different construct 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 123–444（322 aa） Fragment：residues 123-444	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；300 K；Ammonium Sulfate, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50	Resolution 2.80 Å R-free 0.260
2CPT Solution structure of MIT domain from human SKD1 Deposited 2005-05-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–104（104 aa） Fragment：MIT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition 1.11mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3 \| 90% H2O/10% D2O	Resolution not provided
2JQH VPS4B MIT Deposited 2007-06-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–86（86 aa） Fragment：MIT domain, residues 1-86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.65；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 1.8 mM [U-100% 13C; U-100% 15N] VPS4B MIT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JQK VPS4B MIT-CHMP2B Complex Deposited 2007-06-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa） Fragment：MIT domain, residues 1-86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.65；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.48 mM [U-100% 13C; U-100% 15N] VPS4B MIT, 4.8 mM CHMP2B(195-213), 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.84 mM VPS4B MIT, 0.26 mM [U-100% 13C; U-100% 15N] CHMP2B(195-213), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7L9X Structure of VPS4B in complex with an allele-specific covalent inhibitor Deposited 2021-01-05	Different construct 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 1–444（444 aa）	Not recorded	XQV N-{3-[(8-phenyl[1,2,4]triazolo[1,5-a]pyridin-2-yl)amino]phenyl}propanamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；100 mM NH4SO4, 100 mM Hepes pH 7.5, 10% PEG 4000	Resolution 2.81 Å R-free 0.267

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS4B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 1–89

IST1 homolog

Homo sapiens

UniProt P53990

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 341–364	Fragment：UNP residues 341-364	Vacuolar protein sorting-associated protein 4B × 1 （O75351）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.3；299 K；2.58 M Na-malonate	Resolution 2.50 Å R-free 0.271

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 4U7Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FRR Structure of human IST1(NTD) - (residues 1-189)(P21) Deposited 2009-01-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–189（189 aa） Fragment：UNP residues 1-189	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；296 K；35% pentaethritol propexylate 180mM KCl 50 mM HEPES, pH 7.6 7% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.80 Å R-free 0.247
3FRS Structure of human IST1(NTD) (residues 1-189)(p43212) Deposited 2009-01-08	Different construct 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 5–189（185 aa） Fragment：UNP residues 1-189	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；10mM Tris-HCL, pH 8.0, 350mM NaCl, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.61 Å R-free 0.298
3JC1 Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer Deposited 2015-11-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 68 PDB declaration: 68-meric	Chain Aa 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ac 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ae 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ag 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ai 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ak 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Am 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ao 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Aq 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain As 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Au 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Aw 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ay 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ba 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bc 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Be 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bg 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bi 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bk 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bm 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bo 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bq 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bs 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bu 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Bw 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain By 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ca 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Cc 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ce 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Cg 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ci 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Ck 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Cm 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187) Chain Co 6–187（182 aa） Fragment：N-terminal domain (UNP residues 6-187)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 mM Tris, pH 8.0, 25 mM sodium chloride；pH 8；25 mM Tris, pH 8.0, 25 mM sodium chloride cryo-EM vitrification conditions Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset)；Cryogen ETHANE；Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset), and plunged into liquid ethane (VITROBOT MARK III).	Resolution 4.00 Å
4U7E The crystal structure of the complex of LIP5 NTD and IST1 MIM Deposited 2014-07-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 341–364（24 aa） Fragment：UNP residues 341-364	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；30% (w/v) PEG5000MME, 0.1 M ammonium sulfate , 0.1 M MES	Resolution 1.60 Å R-free 0.201
4U7I Structure of the complex of Spartin MIT and IST1 MIM Deposited 2014-07-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 341–364（24 aa） Fragment：UNP residues 341-364	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；277 K；2.9 M Na-malonate	Resolution 1.79 Å R-free 0.220
4WZX ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins Deposited 2014-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 342–364（23 aa） Fragment：MIT-interacting motif (UNP residues 342-364)	Not recorded	CO COBALT (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；50mM MES pH 6.5, 5mM Cobalt chloride, 800mM ammonium sulfate	Resolution 1.39 Å R-free 0.180
6E8G CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution Deposited 2018-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 1–366（366 aa） Chain BA 1–366（366 aa） Chain BB 1–366（366 aa） Chain C 1–366（366 aa） Chain DA 1–366（366 aa） Chain DB 1–366（366 aa） Chain E 1–366（366 aa） Chain FA 1–366（366 aa） Chain FB 1–366（366 aa） Chain G 1–366（366 aa） Chain HA 1–366（366 aa） Chain HB 1–366（366 aa） Chain I 1–366（366 aa） Chain JA 1–366（366 aa） Chain JB 1–366（366 aa） Chain K 1–366（366 aa） Chain LA 1–366（366 aa） Chain LB 1–366（366 aa） Chain M 1–366（366 aa） Chain NA 1–366（366 aa） Chain NB 1–366（366 aa） Chain O 1–366（366 aa） Chain PA 1–366（366 aa） Chain PB 1–366（366 aa） Chain Q 1–366（366 aa） Chain RA 1–366（366 aa） Chain RB 1–366（366 aa） Chain S 1–366（366 aa） Chain TA 1–366（366 aa） Chain TB 1–366（366 aa） Chain V 1–366（366 aa） Chain VA 1–366（366 aa） Chain X 1–366（366 aa） Chain XA 1–366（366 aa） Chain Z 1–366（366 aa） Chain ZA 1–366（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 mm offset with 10 sec wait time and 2-4 sec blot	Resolution 2.90 Å
6TZ4 CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (right-handed) Deposited 2019-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric	Chain 01 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain AA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain AB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain B 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain CA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain CB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain D 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain EA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain EB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain F 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain GA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain GB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain H 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain IA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain IB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain J 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain KA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain KB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain L 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain MA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain MB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain N 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain OA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain OB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain P 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain QA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain QB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain R 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain SA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain SB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain T 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain UA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain W 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain WA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain Y 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain YA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane	Resolution 3.20 Å
6TZ5 CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (left-handed) Deposited 2019-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 68 PDB declaration: 68-meric	Chain A 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain BA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain BB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain C 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain DA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain DB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain E 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain FA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain FB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain G 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain HA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain HB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain I 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain JA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain JB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain K 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain LA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain LB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain M 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain NA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain NB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain O 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain PA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain PB 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain Q 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain RA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain S 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain TA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain V 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain VA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain X 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain XA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain Z 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain ZA 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane	Resolution 3.10 Å
6TZA CryoEM reconstruction of ESCRT-III filament composed of IST1 NTD R16E K27E double mutant Deposited 2019-08-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain B 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain C 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain D 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain E 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain F 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain G 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain H 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain I 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain J 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain K 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain L 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain M 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189) Chain N 1–189（189 aa） Fragment：N-terminal domain (UNP residues 1-189)	Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E Mutation：R16E K27E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane.	Resolution 7.20 Å
7S7J Structure of Human SPASTIN-IST1 complex. Deposited 2021-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 342–364（23 aa） Fragment：UNP residues 342-364	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 CA CALCIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；40% v/v PEG 300, 100 mM Sodium cacodylate / Hydrochloric acid pH=6.5, 200 mM Calcium Acetate	Resolution 1.15 Å R-free 0.157
8UC6 Calpain-7:IST1 Complex Deposited 2023-09-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 335–379（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；294 K；Both proteins were purified and concentrated to 20 mg/ml in buffer containing 25 mM Tris, pH 7.2, 150 mM NaCl, 1 mM TCEP, 0.5 mM EDTA. The proteins were mixed in a 1:2 molar ratio (CAPN7:IST1). Crystals grew at 21 C (294 K) in Rigaku Wizard Cryo condition D5 (25% (v/v) 1,2-Porpanediol, 100 mM Sodium phosphate dibasic/Citric acid pH 4.2, 5% (w/v) PEG 3000, 10% (v/v) Glycerol. Crystals were transferred briefly to crystallization buffer supplemented with 25% added glycerol prior to plunging in liquid nitrogen	Resolution 2.70 Å R-free 0.285
8UC6 Calpain-7:IST1 Complex Deposited 2023-09-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 335–379（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；294 K；Both proteins were purified and concentrated to 20 mg/ml in buffer containing 25 mM Tris, pH 7.2, 150 mM NaCl, 1 mM TCEP, 0.5 mM EDTA. The proteins were mixed in a 1:2 molar ratio (CAPN7:IST1). Crystals grew at 21 C (294 K) in Rigaku Wizard Cryo condition D5 (25% (v/v) 1,2-Porpanediol, 100 mM Sodium phosphate dibasic/Citric acid pH 4.2, 5% (w/v) PEG 3000, 10% (v/v) Glycerol. Crystals were transferred briefly to crystallization buffer supplemented with 25% added glycerol prior to plunging in liquid nitrogen	Resolution 2.70 Å R-free 0.285
8V2Q CHMP1B/IST1 ssRNA bound copolymer Deposited 2023-11-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 182 PDB declaration: 182-meric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8V2R CryoEM of ssDNA bound CHMP1B/IST1 copolymer assembly Deposited 2023-11-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8V2S CHMP1B/IST1 dsDNA bound copolymer Deposited 2023-11-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 192 PDB declaration: 192-meric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å

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

View Construct and Data Evidence

UniProt name	IST1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–24； UniProt 341–364

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	4u7y
Deposition date deposition_date	2014-07-31
Structure title title	Structure of the complex of VPS4B MIT and IST1 MIM
Keywords keywords	complex, MIM1, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	14.95 Å
Radius of gyration Rg (electron density) rg_electron	13.85 Å
Forward intensity I(0) i0	2157720.00
Molecular weight molecular_weight	10110.0 kDa
Excluded volume excluded_volume	12661 Å³
Envelope volume envelope_volume	14873 Å³
Hydration-shell volume shell_volume	9753 Å³
Envelope diameter envelope_diameter	57.9 Å
Shell Rg shell_rg	18.78 Å
Envelope Rg envelope_rg	14.65 Å
Shape Rg shape_rg	13.83 Å
Total Rg total_rg	15.04 Å
Total atoms total_atoms	716
Residues n_residues	96
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	56.9 Å
Rg (real space) rg_real	15.02 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	2.1580e+06
I(0) uncertainty (real space) i0_real_error	2.8900e+04
Rg (reciprocal space) rg_reciprocal	15.02 Å
I(0) (reciprocal space) i0_reciprocal	2158000.0000
Solution quality estimate total_estimate	0.7022
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.551
Kurtosis Kurtosis kurtosis	0.298
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	387900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.464; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.736; Smooth: 0.000

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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	Vacuolar protein sorting-associated protein 4B
Molecular weight formula_weight	10310.7 kDa
EC 编号 ec_number	3.6.4.6
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	722

SMSSTSPNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIRAKCTEYLDRAEKLKEYLKNKEKKAQKPVKE

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 polymer

Description description	IST1 homolog
Molecular weight formula_weight	3009.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

STSASEDIDFDDLSRRFEELKKKTW

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4u7ya_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.14 — MIT domain
Family Family family	a.7.14.1 — MIT domain

CATH v4.4 (1 domains)

Domain ID domain_id	4u7yA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit

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8. Citations (1)

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Unit-cell length a length_a	78.401 Å
Unit-cell length b length_b	78.401 Å
Unit-cell length c length_c	67.642 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 6 2 2
Space-group number int_tables_number	177
Crystal system crystal_system	—

Resolution resolution	2.502 Å
Low-resolution limit resolution_low	33.820 Å
R factor r_factor	0.2276
R_work r_work	0.2252
R_free r_free	0.2713

fit	/app/data/saxs_computation/u7/4u7y/4u7y.fit
pddf	/app/data/pr_computation/u7/4u7y/4u7y.pr.out
profile	/app/data/saxs_computation/u7/4u7y/4u7y.dat

Structure of the complex of VPS4B MIT and IST1 MIM

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

Vacuolar protein sorting-associated protein 4B

State in the Current Structure

Other States of the Same Protein in the Database

IST1 homolog

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)