← Back to search
3um1

Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5

Method: X-RAY DIFFRACTION Dmax: 123.3 Å Quality: REASONABLE
▼

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

BRO1 domain-containing protein BROX

Homo sapiens

UniProt Q5VW32

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–377 Chain D； UniProt 2–377 Fragment：Brox bro1 domain 2-377 Charged multivesicular body protein 5 × 2 （Q9NZZ3） GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.71 Å R-free 0.251

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 3UM1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3R9M Crystal structure of the Brox Bro1 domain Deposited 2011-03-25 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 2–374（373 aa） Fragment：UNP residues 2-374
Not recorded EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M MES, 1M sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.95 Å R-free 0.167
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–411（410 aa） Fragment：brox bro1 domain 2-411
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.211
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–411（410 aa） Fragment：brox bro1 domain 2-411
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.211
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-411
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.257
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-411
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.257
3UM2 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–377（376 aa） Fragment：Brox bro1 domain 2-377
Chain D 2–377（376 aa） Fragment：Brox bro1 domain 2-377
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.241
3UM3 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP4B Deposited 2011-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-377
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；273 K；1.0M sodium citrate, 0.1M imidazol, 15% glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 3.80 Å R-free 0.243
3ZXP Structural and Functional Analyses of the Bro1 Domain Protein BROX Deposited 2011-08-13 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 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401
Chain B 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401
Chain C 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.6；22% PEG 1500, 0.1M MMT 6.6
Resolution 2.50 Å R-free 0.247

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BROX_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–376； UniProt 2–377 Author chain D； PDBConstruct 1–376； UniProt 2–377

Charged multivesicular body protein 5

Homo sapiens

UniProt Q9NZZ3

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 151–219 Chain E； UniProt 151–219 Fragment：C-terminal tail of CHMP5 151-219 BRO1 domain-containing protein BROX × 2 （Q5VW32） GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.71 Å R-free 0.251

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 3UM1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LXM Lip5-chmp5 Deposited 2012-08-29 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 × 2 PDB declaration: dimeric
Chain B 139–195（57 aa） Fragment：UNP residues 139-195
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 75；Pressure ambient
NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] LIP5(1-168), 0.5 mM [U-100% 13C; U-100% 15N] CHMP5(139-195), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O | 92% H2O/8% D2O
Resolution not provided
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 151–219（69 aa） Fragment：C-terminal tails of CHMP5 151-219
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.211
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 151–219（69 aa） Fragment：C-terminal tails of CHMP5 151-219
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.211
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 200–219（20 aa） Fragment：Synthetic peptide of C-terminal tail of CHMP5 200-219
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.257
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 200–219（20 aa） Fragment：Synthetic peptide of C-terminal tail of CHMP5 200-219
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.257
3UM2 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 200–219（20 aa） Fragment：Synthetic peptide of C-terminal tail of CHMP5 200-219
Chain E 200–219（20 aa） Fragment：Synthetic peptide of C-terminal tail of CHMP5 200-219
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.59 Å R-free 0.241
4TXR Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM Deposited 2014-07-04 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 139–195（57 aa） Fragment：UNP residues 139-195
Not recorded ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；19% PEG 4000, 0.025 M sodium acetate
Resolution 1.00 Å R-free 0.180

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHMP5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–69； UniProt 151–219 Author chain E； PDBConstruct 1–69； UniProt 151–219

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 3um1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3um1
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3um1
Deposition date deposition_date2011-11-11
Structure title titleCrystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5
Keywords keywordsbeta hairpin, ESCRT-III, CHMPs, MEMBRANE PROTEIN-TRANSPORT PROTEIN complex, BROX; MEMBRANE PROTEIN/TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier35.24 Å
Radius of gyration Rg (electron density) rg_electron34.97 Å
Forward intensity I(0) i0116525000.00
Molecular weight molecular_weight88471.0 kDa
Excluded volume excluded_volume111620 ų
Envelope volume envelope_volume146620 ų
Hydration-shell volume shell_volume36317 ų
Envelope diameter envelope_diameter128.3 Å
Shell Rg shell_rg39.62 Å
Envelope Rg envelope_rg34.46 Å
Shape Rg shape_rg34.97 Å
Total Rg total_rg35.36 Å
Total atoms total_atoms6244
Residues n_residues784
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
▼

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

Maximum dimension Dmax dmax123.3 Å
Rg (real space) rg_real35.42 Å
Rg uncertainty (real space) rg_real_error1.12 Å
I(0) (real space) i0_real1.1650e+08
I(0) uncertainty (real space) i0_real_error2.0650e+06
Rg (reciprocal space) rg_reciprocal35.31 Å
I(0) (reciprocal space) i0_reciprocal116500000.0000
Solution quality estimate total_estimate0.6766
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.9 Å
Skewness Skewness skewness0.456
Kurtosis Kurtosis kurtosis-0.192
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17780000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.873; Smooth: 0.924
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3um1A00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily280 — alix/aip1 like domains
Domain ID domain_id3um1D00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily280 — alix/aip1 like domains
▶

8. Citations (1)

▶

9. Files and Curves (10)