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2jqk

VPS4B MIT-CHMP2B Complex

Method: SOLUTION NMR Dmax: 44.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar protein sorting-associating protein 4B

Homo sapiens

UniProt O75351

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 1–86 Fragment：MIT domain, residues 1-86 Charged multivesicular body protein 2b × 1 （Q9UQN3） 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

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 2JQK 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 conditions 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 method 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 conditions 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 oligomeric state Different experimental conditions 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
4U7Y Structure of the complex of VPS4B MIT and IST1 MIM Deposited 2014-07-31 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–89（89 aa） Fragment：MIT domain (UNP residues 1-89)
Not recorded No recorded non-water small molecule 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
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 method 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 4–89； UniProt 1–86

Charged multivesicular body protein 2b

Homo sapiens

UniProt Q9UQN3

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 195–213 Fragment：C-terminal sequence database residues 195-213 Vacuolar protein sorting-associating protein 4B × 1 （O75351） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name CHM2B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–19； UniProt 195–213

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

SAXS profile for 2jqk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2jqk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2jqk
Deposition date deposition_date2007-06-02
Structure title titleVPS4B MIT-CHMP2B Complex
Keywords keywordsCHMP2B, VPS4B MIT, Complex, Four Helix Bundle, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.28 Å
Radius of gyration Rg (electron density) rg_electron13.04 Å
Forward intensity I(0) i0556174000.00
Molecular weight molecular_weight198300.0 kDa
Excluded volume excluded_volume247830 ų
Envelope volume envelope_volume21886 ų
Hydration-shell volume shell_volume12830 ų
Envelope diameter envelope_diameter50.1 Å
Shell Rg shell_rg20.28 Å
Envelope Rg envelope_rg14.83 Å
Shape Rg shape_rg13.03 Å
Total Rg total_rg13.25 Å
Total atoms total_atoms27920
Residues n_residues1720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax44.7 Å
Rg (real space) rg_real13.26 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real5.5620e+08
I(0) uncertainty (real space) i0_real_error6.3710e+06
Rg (reciprocal space) rg_reciprocal13.26 Å
I(0) (reciprocal space) i0_reciprocal556200000.0000
Solution quality estimate total_estimate0.7925
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.3 Å
Skewness Skewness skewness0.286
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000
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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

SCOP 2.08 (1 domains)

Domain ID domain_idd2jqka_
Class classa — All alpha proteins
Fold Fold folda.7 — Spectrin repeat-like
Superfamily Superfamily superfamilya.7.14 — MIT domain
Family Family familya.7.14.1 — MIT domain

CATH v4.4 (1 domains)

Domain ID domain_id2jqkA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit
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8. Citations (1)

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9. Files and Curves (10)