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4jjy

Alix V domain

Method: X-RAY DIFFRACTION Dmax: 160.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death 6-interacting protein

Homo sapiens

UniProt Q8WUM4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 355–708 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 6.50 Å R-free 0.283
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 355–708 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 6.50 Å R-free 0.283

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 4JJY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2OEV Crystal structure of ALIX/AIP1 Deposited 2007-01-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–698（698 aa） Fragment：Bro1-V Domains, residues 1-698
Mutation：K268Y, K269Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；286 K；8% PEG 4000, 0.1M ammonium acetate, 0.1M magnesium acetate, 0.05M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 3.30 Å R-free 0.317
2OEW Structure of ALIX/AIP1 Bro1 Domain Deposited 2007-01-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–359（359 aa） Fragment：Bro1 Domain, residues 1-359
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；286 K；10% PEG 20000, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 2.55 Å R-free 0.274
2OEX Structure of ALIX/AIP1 V Domain Deposited 2007-01-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 360–702（343 aa） Fragment：V Domain, residues 359-702
Chain B 360–702（343 aa） Fragment：V Domain, residues 359-702
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, SITTING DROP；pH 8；277 K；14% PEG 3350, 0.16M magnesium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.58 Å R-free 0.302
2OJQ Crystal structure of Alix V domain Deposited 2007-01-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 360–702（343 aa） Fragment：V domain, residues 360-702
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 8.5；13-15% PEG 6000, 6-10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Resolution 2.87 Å R-free 0.318
2R02 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLTSL Late Domain Deposited 2007-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains
Mutation：K268Y,K269Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions sitting drop vapor diffusion；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, sitting drop vapor diffusion, temperature 286K
Resolution 2.60 Å R-free 0.285
2R03 Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain Deposited 2007-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains
Mutation：K268Y,K269Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 2.59 Å R-free 0.286
2R05 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain Deposited 2007-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains
Mutation：K268Y,K269Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 2.55 Å R-free 0.280
2XS1 Crystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL Late Domain Deposited 2010-09-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；6.5% PEG4000, 0.2 MGCL2, 0.1M MES PH 6.2
Resolution 2.30 Å R-free 0.252
2XS8 Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain Deposited 2010-09-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；6.1% PEG4000, 0.2M MGCL2, 0.1M MES PH 6.1
Resolution 2.50 Å R-free 0.261
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22 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 C 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814
Mutation：C15S ZN ZINC ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814
Mutation：C15S ZN ZINC ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814
Chain D 799–814（16 aa） Fragment：ALG-2 binding site, residues 799-814
Mutation：C15S Mutation：C15S ZN ZINC ION × 8 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.274
3C3O ALIX Bro1-domain:CHMIP4A co-crystal structure Deposited 2008-01-28 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 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-358)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.15 Å R-free 0.284
3C3Q ALIX Bro1-domain:CHMIP4B co-crystal structure Deposited 2008-01-28 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 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.290
3C3R ALIX BRO1 CHMP4C complex Deposited 2008-01-28 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 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；10% PEG 2,000, 100mM Na MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.02 Å R-free 0.288
3E1R Midbody targeting of the ESCRT machinery by a non-canonical coiled-coil in CEP55 Deposited 2008-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 797–809（13 aa） Fragment：UNP residues 797-809
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；100 mM MES, 22% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.00 Å R-free 0.248
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 796–809（14 aa）
Mutation：P796D/P807I/G808P/Y809P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.79 Å R-free 0.227
5V3R CHMP4C in complex with ALIX BRO1 Deposited 2017-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–359（359 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；10% PEG20000, 100 mM MES, pH 6.5
Resolution 1.91 Å R-free 0.213
5WA1 CHMP4C A232T in complex with ALIX BRO1 Deposited 2017-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–358（358 aa） Fragment：Bro1 domain (UNP residues 1-358)
Mutation：A232T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；15% PEG8000, 100 mM MES, pH 6.5, 200 mM sodium acetate
Resolution 1.87 Å R-free 0.215
6KP3 STRUCTURE OF SENDAI VIRUS Y3/ALIX-BRO1 DOMAIN COMPLEX Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–359（359 aa） Fragment：bro1 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.45；297 K；15% PEG 3350, 0.2M Sodium Malonate-NaOH
Resolution 2.20 Å R-free 0.262

18 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDC6I_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–360； UniProt 355–708 Author chain B； PDBConstruct 6–360； UniProt 355–708

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 4jjy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jjy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jjy
Deposition date deposition_date2013-03-08
Structure title titleAlix V domain
Keywords keywordsUbiquitin, Endosome, Membrane Trafficking, virus budding, ESCRTI, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.23 Å
Radius of gyration Rg (electron density) rg_electron45.48 Å
Forward intensity I(0) i096988500.00
Molecular weight molecular_weight77210.0 kDa
Excluded volume excluded_volume95933 ų
Envelope volume envelope_volume177170 ų
Hydration-shell volume shell_volume36333 ų
Envelope diameter envelope_diameter158.0 Å
Shell Rg shell_rg44.03 Å
Envelope Rg envelope_rg44.04 Å
Shape Rg shape_rg45.42 Å
Total Rg total_rg45.58 Å
Total atoms total_atoms5396
Residues n_residues676
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 dmax160.4 Å
Rg (real space) rg_real45.56 Å
Rg uncertainty (real space) rg_real_error2.45 Å
I(0) (real space) i0_real9.6990e+07
I(0) uncertainty (real space) i0_real_error1.9200e+06
Rg (reciprocal space) rg_reciprocal45.24 Å
I(0) (reciprocal space) i0_reciprocal96950000.0000
Solution quality estimate total_estimate0.5953
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.4 Å
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-0.281
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3813000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.901; Smooth: 0.842
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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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9. Files and Curves (10)