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2lxm

Lip5-chmp5

Method: SOLUTION NMR Dmax: 58.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar protein sorting-associated protein VTA1 homolog

Homo sapiens

UniProt Q9NP79

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 1–168 Fragment：UNP residues 1-168 Charged multivesicular body protein 5 × 1 （Q9NZZ3） 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

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 2LXM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LXL Lip5(mit)2 Deposited 2012-08-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–183（183 aa） Fragment：UNP residues 1-183
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 0.075；Pressure ambient
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] LIP5(1-183), 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
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04 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 1–162（162 aa） Fragment：UNP residues 1-162
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate
Resolution 3.01 Å R-free 0.286
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–162（162 aa） Fragment：UNP residues 1-162
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate
Resolution 3.01 Å R-free 0.286
4TXP Crystal structure of LIP5 N-terminal domain Deposited 2014-07-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–162（162 aa） Fragment：UNP residues 1-162
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；7.5-9% PEG 8000, 20% 1,4 butanediol, 0.1M cacodylate, 0.2M sodium acetate
Resolution 3.01 Å R-free 0.286
4TXQ Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM Deposited 2014-07-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–162（162 aa） Fragment：UNP residues 1-162
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris
Resolution 2.21 Å R-free 0.227
4TXQ Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM Deposited 2014-07-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–162（162 aa） Fragment：UNP residues 1-162
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277.15 K；Protein mixture was added in 1:1 ratio with a solution of 16% MPD, 0.1 M Tris and equilibrated against a mother liquid of 8% MPD, 0.1 M Tris
Resolution 2.21 Å R-free 0.227
4TXR Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM Deposited 2014-07-04 Different construct 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 A 1–162（162 aa） Fragment：UNP residues 1-162
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
4U7E The crystal structure of the complex of LIP5 NTD and IST1 MIM Deposited 2014-07-30 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–162（162 aa） Fragment：N-terminal domain (UNP residues 1-162)
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

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

View Construct and Data Evidence
UniProt name VTA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–168； UniProt 1–168

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 139–195 Fragment：UNP residues 139-195 Vacuolar protein sorting-associated protein VTA1 homolog × 1 （Q9NP79） 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

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 2LXM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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
3UM1 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 ligand/ion Different experimental method 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 tail of CHMP5 151-219
Chain E 151–219（69 aa） Fragment：C-terminal tail 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 2.71 Å R-free 0.251
3UM2 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-12 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 × 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 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 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 3–59； UniProt 139–195

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 2lxm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2lxm
Deposition date deposition_date2012-08-29
Structure title titleLip5-chmp5
Keywords keywordsMIT, 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_guinier18.03 Å
Radius of gyration Rg (electron density) rg_electron17.64 Å
Forward intensity I(0) i0734007000.00
Molecular weight molecular_weight225570.0 kDa
Excluded volume excluded_volume280840 ų
Envelope volume envelope_volume47568 ų
Hydration-shell volume shell_volume20773 ų
Envelope diameter envelope_diameter61.5 Å
Shell Rg shell_rg25.64 Å
Envelope Rg envelope_rg19.17 Å
Shape Rg shape_rg17.61 Å
Total Rg total_rg17.93 Å
Total atoms total_atoms31320
Residues n_residues1990
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 dmax58.2 Å
Rg (real space) rg_real17.96 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real7.3400e+08
I(0) uncertainty (real space) i0_real_error9.5790e+06
Rg (reciprocal space) rg_reciprocal17.97 Å
I(0) (reciprocal space) i0_reciprocal734000000.0000
Solution quality estimate total_estimate0.8069
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.6 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.324
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1263000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2lxmA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily270 — Vacuolar protein sorting-associated protein vta1
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8. Citations (1)

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9. Files and Curves (10)