SAXSdb — 9bw6

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

Major vault protein

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 × 156 PDB declaration: 156-meric（156） Consistent with protein copy count	Chain A； UniProt 1–893 Chain C； UniProt 1–893	Not recorded	Protein mono-ADP-ribosyltransferase PARP4 × 78 （Q9UKK3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–893 Chain C； UniProt 1–893	Not recorded	Protein mono-ADP-ribosyltransferase PARP4 × 2 （Q9UKK3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å

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 9BW6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11DR Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766) Deposited 2026-02-18	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 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
11DV RNA Vault waist region, focused refinement (MVP/TEP1 sample) Deposited 2026-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa） Chain D 1–893（893 aa） Chain E 1–893（893 aa） Chain F 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris 7.5 75 NaCl 1.5 mM MgCl2 1 mM DTT 1 mM BAD 1 mM AMP-PNP 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.33 Å
11EE RNA Vault shoulder region with BAD bound, focused refinement (MVP/TEP1 sample) Deposited 2026-02-18	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 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	DQV [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris 7.5 75 NaCl 1.5 mM MgCl2 1 mM DTT 1 mM BAD 1 mM AMP-PNP 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.87 Å
11EQ RNA Vault with BAD bound (MVP/TEP1 sample) Deposited 2026-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain 0 1–893（893 aa） Chain 1 1–893（893 aa） Chain 2 1–893（893 aa） Chain 3 1–893（893 aa） Chain 4 1–893（893 aa） Chain 5 1–893（893 aa） Chain 6 1–893（893 aa） Chain 7 1–893（893 aa） Chain 8 1–893（893 aa） Chain 9 1–893（893 aa） Chain A 1–893（893 aa） Chain AA 1–893（893 aa） Chain AB 1–893（893 aa） Chain AC 1–893（893 aa） Chain AD 1–893（893 aa） Chain AE 1–893（893 aa） Chain AF 1–893（893 aa） Chain AG 1–893（893 aa） Chain AH 1–893（893 aa） Chain AI 1–893（893 aa） Chain AJ 1–893（893 aa） Chain AK 1–893（893 aa） Chain AL 1–893（893 aa） Chain AM 1–893（893 aa） Chain AN 1–893（893 aa） Chain AO 1–893（893 aa） Chain AP 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa） Chain D 1–893（893 aa） Chain E 1–893（893 aa） Chain F 1–893（893 aa） Chain G 1–893（893 aa） Chain H 1–893（893 aa） Chain I 1–893（893 aa） Chain J 1–893（893 aa） Chain K 1–893（893 aa） Chain L 1–893（893 aa） Chain M 1–893（893 aa） Chain N 1–893（893 aa） Chain O 1–893（893 aa） Chain P 1–893（893 aa） Chain Q 1–893（893 aa） Chain R 1–893（893 aa） Chain S 1–893（893 aa） Chain T 1–893（893 aa） Chain U 1–893（893 aa） Chain V 1–893（893 aa） Chain W 1–893（893 aa） Chain X 1–893（893 aa） Chain Y 1–893（893 aa） Chain Z 1–893（893 aa） Chain a 1–893（893 aa） Chain b 1–893（893 aa） Chain c 1–893（893 aa） Chain d 1–893（893 aa） Chain e 1–893（893 aa） Chain f 1–893（893 aa） Chain g 1–893（893 aa） Chain h 1–893（893 aa） Chain i 1–893（893 aa） Chain j 1–893（893 aa） Chain k 1–893（893 aa） Chain l 1–893（893 aa） Chain m 1–893（893 aa） Chain n 1–893（893 aa） Chain o 1–893（893 aa） Chain p 1–893（893 aa） Chain q 1–893（893 aa） Chain r 1–893（893 aa） Chain s 1–893（893 aa） Chain t 1–893（893 aa） Chain u 1–893（893 aa） Chain v 1–893（893 aa） Chain w 1–893（893 aa） Chain x 1–893（893 aa） Chain y 1–893（893 aa） Chain z 1–893（893 aa）	Not recorded	DQV [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM Tris 7.5 75 NaCl 1.5 mM MgCl2 1 mM DTT 1 mM BAD 1 mM AMP-PNP 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.17 Å
11FH RNA Vault cap (MVP/PARP4/TEP1 sample) Deposited 2026-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric	Chain A 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa） Chain D 1–893（893 aa） Chain E 1–893（893 aa） Chain F 1–893（893 aa） Chain G 1–893（893 aa） Chain H 1–893（893 aa） Chain I 1–893（893 aa） Chain J 1–893（893 aa） Chain K 1–893（893 aa） Chain L 1–893（893 aa） Chain M 1–893（893 aa） Chain N 1–893（893 aa） Chain O 1–893（893 aa） Chain P 1–893（893 aa） Chain Q 1–893（893 aa） Chain R 1–893（893 aa） Chain S 1–893（893 aa） Chain T 1–893（893 aa） Chain U 1–893（893 aa） Chain V 1–893（893 aa） Chain W 1–893（893 aa） Chain X 1–893（893 aa） Chain Y 1–893（893 aa） Chain Z 1–893（893 aa） Chain a 1–893（893 aa） Chain b 1–893（893 aa） Chain c 1–893（893 aa） Chain d 1–893（893 aa） Chain e 1–893（893 aa） Chain f 1–893（893 aa） Chain g 1–893（893 aa） Chain h 1–893（893 aa） Chain i 1–893（893 aa） Chain j 1–893（893 aa） Chain k 1–893（893 aa） Chain l 1–893（893 aa） Chain m 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris 150 mM NaCl 1 mM DTT 1 mM NADP 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.92 Å
11JB RNA Vault with ADPR bound (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain 0 1–893（893 aa） Chain 1 1–893（893 aa） Chain 2 1–893（893 aa） Chain 3 1–893（893 aa） Chain 4 1–893（893 aa） Chain 5 1–893（893 aa） Chain 6 1–893（893 aa） Chain 7 1–893（893 aa） Chain 8 1–893（893 aa） Chain 9 1–893（893 aa） Chain A 1–893（893 aa） Chain AA 1–893（893 aa） Chain AB 1–893（893 aa） Chain AC 1–893（893 aa） Chain AD 1–893（893 aa） Chain AE 1–893（893 aa） Chain AF 1–893（893 aa） Chain AG 1–893（893 aa） Chain AH 1–893（893 aa） Chain AI 1–893（893 aa） Chain AJ 1–893（893 aa） Chain AK 1–893（893 aa） Chain AL 1–893（893 aa） Chain AM 1–893（893 aa） Chain AN 1–893（893 aa） Chain AO 1–893（893 aa） Chain AP 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa） Chain D 1–893（893 aa） Chain E 1–893（893 aa） Chain F 1–893（893 aa） Chain G 1–893（893 aa） Chain H 1–893（893 aa） Chain I 1–893（893 aa） Chain J 1–893（893 aa） Chain K 1–893（893 aa） Chain L 1–893（893 aa） Chain M 1–893（893 aa） Chain N 1–893（893 aa） Chain O 1–893（893 aa） Chain P 1–893（893 aa） Chain Q 1–893（893 aa） Chain R 1–893（893 aa） Chain S 1–893（893 aa） Chain T 1–893（893 aa） Chain U 1–893（893 aa） Chain V 1–893（893 aa） Chain W 1–893（893 aa） Chain X 1–893（893 aa） Chain Y 1–893（893 aa） Chain Z 1–893（893 aa） Chain a 1–893（893 aa） Chain b 1–893（893 aa） Chain c 1–893（893 aa） Chain d 1–893（893 aa） Chain e 1–893（893 aa） Chain f 1–893（893 aa） Chain g 1–893（893 aa） Chain h 1–893（893 aa） Chain i 1–893（893 aa） Chain j 1–893（893 aa） Chain k 1–893（893 aa） Chain l 1–893（893 aa） Chain m 1–893（893 aa） Chain n 1–893（893 aa） Chain o 1–893（893 aa） Chain p 1–893（893 aa） Chain q 1–893（893 aa） Chain r 1–893（893 aa） Chain s 1–893（893 aa） Chain t 1–893（893 aa） Chain u 1–893（893 aa） Chain v 1–893（893 aa） Chain w 1–893（893 aa） Chain x 1–893（893 aa） Chain y 1–893（893 aa） Chain z 1–893（893 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.16 Å
11JC RNA Vault Shoulder with ADPR bound, compact conformation, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	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 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.96 Å
11JD RNA Vault Shoulder with ADPR bound, extended conformation, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	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 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.37 Å
11JF RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
1Y7X Solution structure of a two-repeat fragment of major vault protein Deposited 2004-12-10	Different construct Different mutation/modification 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 113–221（109 aa） Fragment：domains 3-4 of MVP repeats (residues 113-221)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient NMR sample composition 1mM MVP U-15N, 20mM bis-Tris, 150mM NaCl, 2mM CaCl2, 15mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM MVP, 20mM bis-Tris, 150mM NaCl, 2mM CaCl2, 15mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BW5 Human Vault Cage Deposited 2024-05-20	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 3.30 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric	Chain A 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different ligand/ion	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–893（893 aa） Chain C 1–893（893 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9MXH Human Vault Cage in complex with NAD+ Deposited 2025-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES pH 8, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9MXJ Human Vault Cage in complex with ADP-ribose Deposited 2025-01-20	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	APR ADENOSINE-5-DIPHOSPHORIBOSE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 3.49 Å
9MXJ Human Vault Cage in complex with ADP-ribose Deposited 2025-01-20	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	APR ADENOSINE-5-DIPHOSPHORIBOSE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 3.49 Å
9MXJ Human Vault Cage in complex with ADP-ribose Deposited 2025-01-20	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	APR ADENOSINE-5-DIPHOSPHORIBOSE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 3.49 Å
9MXV Human Vault Cage in complex with ADP Deposited 2025-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES pH 8.0, 5 mM CaCl2, 5 mM MgCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
9MXV Human Vault Cage in complex with ADP Deposited 2025-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES pH 8.0, 5 mM CaCl2, 5 mM MgCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
9MXV Human Vault Cage in complex with ADP Deposited 2025-01-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–893（893 aa） Chain B 1–893（893 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES pH 8.0, 5 mM CaCl2, 5 mM MgCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
9QW9 Human vault protein - primed conformation Deposited 2025-04-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain AA 1–893（893 aa） Chain AB 1–893（893 aa） Chain AC 1–893（893 aa） Chain B 1–893（893 aa） Chain BA 1–893（893 aa） Chain BB 1–893（893 aa） Chain C 1–893（893 aa） Chain CA 1–893（893 aa） Chain CB 1–893（893 aa） Chain D 1–893（893 aa） Chain DA 1–893（893 aa） Chain DB 1–893（893 aa） Chain E 1–893（893 aa） Chain EA 1–893（893 aa） Chain EB 1–893（893 aa） Chain F 1–893（893 aa） Chain FA 1–893（893 aa） Chain FB 1–893（893 aa） Chain G 1–893（893 aa） Chain GA 1–893（893 aa） Chain GB 1–893（893 aa） Chain H 1–893（893 aa） Chain HA 1–893（893 aa） Chain HB 1–893（893 aa） Chain I 1–893（893 aa） Chain IA 1–893（893 aa） Chain IB 1–893（893 aa） Chain J 1–893（893 aa） Chain JA 1–893（893 aa） Chain JB 1–893（893 aa） Chain K 1–893（893 aa） Chain KA 1–893（893 aa） Chain KB 1–893（893 aa） Chain L 1–893（893 aa） Chain LA 1–893（893 aa） Chain LB 1–893（893 aa） Chain M 1–893（893 aa） Chain MA 1–893（893 aa） Chain MB 1–893（893 aa） Chain N 1–893（893 aa） Chain NA 1–893（893 aa） Chain NB 1–893（893 aa） Chain O 1–893（893 aa） Chain OA 1–893（893 aa） Chain OB 1–893（893 aa） Chain P 1–893（893 aa） Chain PA 1–893（893 aa） Chain PB 1–893（893 aa） Chain Q 1–893（893 aa） Chain QA 1–893（893 aa） Chain QB 1–893（893 aa） Chain R 1–893（893 aa） Chain RA 1–893（893 aa） Chain RB 1–893（893 aa） Chain S 1–893（893 aa） Chain SA 1–893（893 aa） Chain SB 1–893（893 aa） Chain T 1–893（893 aa） Chain TA 1–893（893 aa） Chain TB 1–893（893 aa） Chain UA 1–893（893 aa） Chain UB 1–893（893 aa） Chain V 1–893（893 aa） Chain VA 1–893（893 aa） Chain VB 1–893（893 aa） Chain W 1–893（893 aa） Chain WA 1–893（893 aa） Chain WB 1–893（893 aa） Chain X 1–893（893 aa） Chain XA 1–893（893 aa） Chain XB 1–893（893 aa） Chain Y 1–893（893 aa） Chain YA 1–893（893 aa） Chain YB 1–893（893 aa） Chain Z 1–893（893 aa） Chain ZA 1–893（893 aa） Chain ZB 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 1mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9QWQ Human vault protein - committed conformation Deposited 2025-04-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain A 1–893（893 aa） Chain AA 1–893（893 aa） Chain AB 1–893（893 aa） Chain AC 1–893（893 aa） Chain B 1–893（893 aa） Chain BA 1–893（893 aa） Chain BB 1–893（893 aa） Chain C 1–893（893 aa） Chain CA 1–893（893 aa） Chain CB 1–893（893 aa） Chain D 1–893（893 aa） Chain DA 1–893（893 aa） Chain DB 1–893（893 aa） Chain E 1–893（893 aa） Chain EA 1–893（893 aa） Chain EB 1–893（893 aa） Chain F 1–893（893 aa） Chain FA 1–893（893 aa） Chain FB 1–893（893 aa） Chain G 1–893（893 aa） Chain GA 1–893（893 aa） Chain GB 1–893（893 aa） Chain H 1–893（893 aa） Chain HA 1–893（893 aa） Chain HB 1–893（893 aa） Chain I 1–893（893 aa） Chain IA 1–893（893 aa） Chain IB 1–893（893 aa） Chain J 1–893（893 aa） Chain JA 1–893（893 aa） Chain JB 1–893（893 aa） Chain K 1–893（893 aa） Chain KA 1–893（893 aa） Chain KB 1–893（893 aa） Chain L 1–893（893 aa） Chain LA 1–893（893 aa） Chain LB 1–893（893 aa） Chain M 1–893（893 aa） Chain MA 1–893（893 aa） Chain MB 1–893（893 aa） Chain N 1–893（893 aa） Chain NA 1–893（893 aa） Chain NB 1–893（893 aa） Chain O 1–893（893 aa） Chain OA 1–893（893 aa） Chain OB 1–893（893 aa） Chain P 1–893（893 aa） Chain PA 1–893（893 aa） Chain PB 1–893（893 aa） Chain Q 1–893（893 aa） Chain QA 1–893（893 aa） Chain QB 1–893（893 aa） Chain R 1–893（893 aa） Chain RA 1–893（893 aa） Chain RB 1–893（893 aa） Chain S 1–893（893 aa） Chain SA 1–893（893 aa） Chain SB 1–893（893 aa） Chain T 1–893（893 aa） Chain TA 1–893（893 aa） Chain TB 1–893（893 aa） Chain UA 1–893（893 aa） Chain UB 1–893（893 aa） Chain V 1–893（893 aa） Chain VA 1–893（893 aa） Chain VB 1–893（893 aa） Chain W 1–893（893 aa） Chain WA 1–893（893 aa） Chain WB 1–893（893 aa） Chain X 1–893（893 aa） Chain XA 1–893（893 aa） Chain XB 1–893（893 aa） Chain Y 1–893（893 aa） Chain YA 1–893（893 aa） Chain YB 1–893（893 aa） Chain Z 1–893（893 aa） Chain ZA 1–893（893 aa） Chain ZB 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 1mM TCEP, pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.45 Å
9R86 Major Vault Protein from Human Brain Deposited 2025-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric	Chain A0 1–893（893 aa） Chain A1 1–893（893 aa） Chain A2 1–893（893 aa） Chain A3 1–893（893 aa） Chain A4 1–893（893 aa） Chain A5 1–893（893 aa） Chain A6 1–893（893 aa） Chain A7 1–893（893 aa） Chain A8 1–893（893 aa） Chain A9 1–893（893 aa） Chain Ac 1–893（893 aa） Chain Ad 1–893（893 aa） Chain Ae 1–893（893 aa） Chain Af 1–893（893 aa） Chain Ag 1–893（893 aa） Chain Ah 1–893（893 aa） Chain Ai 1–893（893 aa） Chain Aj 1–893（893 aa） Chain Ak 1–893（893 aa） Chain Al 1–893（893 aa） Chain Am 1–893（893 aa） Chain An 1–893（893 aa） Chain Ap 1–893（893 aa） Chain Aq 1–893（893 aa） Chain Ar 1–893（893 aa） Chain As 1–893（893 aa） Chain At 1–893（893 aa） Chain Au 1–893（893 aa） Chain Av 1–893（893 aa） Chain Aw 1–893（893 aa） Chain Ax 1–893（893 aa） Chain Ay 1–893（893 aa） Chain Az 1–893（893 aa） Chain BA 1–893（893 aa） Chain BB 1–893（893 aa） Chain BC 1–893（893 aa） Chain BD 1–893（893 aa） Chain BE 1–893（893 aa） Chain BF 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9R87 Cap of the vault protein from Human Brain Deposited 2025-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric	Chain A 1–893（893 aa） Chain A1 1–893（893 aa） Chain A2 1–893（893 aa） Chain A3 1–893（893 aa） Chain A4 1–893（893 aa） Chain Ar 1–893（893 aa） Chain As 1–893（893 aa） Chain At 1–893（893 aa） Chain Au 1–893（893 aa） Chain Av 1–893（893 aa） Chain Aw 1–893（893 aa） Chain Ax 1–893（893 aa） Chain Ay 1–893（893 aa） Chain Az 1–893（893 aa） Chain B 1–893（893 aa） Chain C 1–893（893 aa） Chain D 1–893（893 aa） Chain E 1–893（893 aa） Chain F 1–893（893 aa） Chain G 1–893（893 aa） Chain H 1–893（893 aa） Chain I 1–893（893 aa） Chain J 1–893（893 aa） Chain K 1–893（893 aa） Chain L 1–893（893 aa） Chain M 1–893（893 aa） Chain N 1–893（893 aa） Chain O 1–893（893 aa） Chain P 1–893（893 aa） Chain Q 1–893（893 aa） Chain R 1–893（893 aa） Chain S 1–893（893 aa） Chain T 1–893（893 aa） Chain U 1–893（893 aa） Chain V 1–893（893 aa） Chain W 1–893（893 aa） Chain X 1–893（893 aa） Chain Y 1–893（893 aa） Chain Z 1–893（893 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

19 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MVP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–893； UniProt 1–893 Author chain C； PDBConstruct 1–893； UniProt 1–893

Protein mono-ADP-ribosyltransferase PARP4

Homo sapiens

UniProt Q9UKK3

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 × 156 PDB declaration: 156-meric（156） Consistent with protein copy count	Chain B； UniProt 1–1724 Chain D； UniProt 1–1724	Not recorded	Major vault protein × 78 （Q14764）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–1724 Chain D； UniProt 1–1724	Not recorded	Major vault protein × 2 （Q14764）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å

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 9BW6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11JF RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample) Deposited 2026-02-26	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 P 1–1724（1724 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	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 242–282（41 aa） Chain A 365–573（209 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–282（41 aa） Chain B 365–573（209 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWY PARP4 ART domain bound to NADH Deposited 2023-05-19	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 242–282（41 aa） Chain C 365–573（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG3350, 0.2M sodium citrate tribasic dihydrate, 1% ethylene glycol, 800uM NADH	Resolution 2.55 Å R-free 0.254
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	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 242–282（41 aa） Chain A 365–573（209 aa）	Not recorded	GOL GLYCEROL × 1 UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–282（41 aa） Chain B 365–573（209 aa）	Not recorded	GOL GLYCEROL × 1 UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SWZ PARP4 ART domain bound to EB47 Deposited 2023-05-19	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 242–282（41 aa） Chain C 365–573（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47	Resolution 3.00 Å R-free 0.248
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification 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 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification 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 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification 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 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX1 PARP4 catalytic domain Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 242–573（332 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350 and 0.1 M Bis-Tris pH 6.5	Resolution 4.20 Å R-free 0.331
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19	Different construct Different mutation/modification 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 242–573（332 aa）	Not recorded	UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47	Resolution 2.95 Å R-free 0.262
8SX2 PARP4 catalytic domain bound to EB47 Deposited 2023-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 242–573（332 aa）	Not recorded	UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM EB47	Resolution 2.95 Å R-free 0.262
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different ligand/ion	Assembly 1 Protein heterocomplex Heteromer；Protein × 156 PDB declaration: 156-meric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 78	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9BW7 Human Vault Cage in complex with PARP4 and NAD+ Deposited 2024-05-20	Different ligand/ion	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1724（1724 aa） Chain D 1–1724（1724 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out under standard conditions	Resolution 2.90 Å
9DEV PARP4 BRCT domain Deposited 2024-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 0.15M Citric Acid pH3.5	Resolution 1.75 Å R-free 0.188
9DFO PARP4 BRCT domain K31Q mutant Deposited 2024-08-30	Different construct Different mutation/modification 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 1–100（100 aa）	Mutation：K31Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；31% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.90 Å R-free 0.208
9DFP PARP4 BRCT domain K23/24Q mutant Deposited 2024-08-30	Different construct Different mutation/modification 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 1–100（100 aa）	Mutation：K23Q,K24Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.92 Å R-free 0.219
9DFQ PARP4 BRCT domain F39Q mutant Deposited 2024-08-30	Different construct Different mutation/modification 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 1–100（100 aa）	Mutation：F39Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2 M ammonium sulfate and 0.1 M sodium acetate pH 4.6	Resolution 2.10 Å R-free 0.230
9DFR PARP4 BRCT domain F39A mutant Deposited 2024-08-30	Different construct Different mutation/modification 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 1–100（100 aa）	Mutation：F39A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6	Resolution 1.90 Å R-free 0.218

11 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PARP4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1724； UniProt 1–1724 Author chain D； PDBConstruct 1–1724； UniProt 1–1724

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	9bw6
Deposition date deposition_date	2024-05-20
Structure title title	Human Vault Cage in complex with PARP4
Keywords keywords	;Vault, Vault Cage, MVP, Major Vault Protein, SPFH, PARP4, Poly(ADP-ribose)Polymerase 4, MINT, Poly(ADP-ribose)Polymerase, Ribonucleoprotein, Megadalton complex, TEP1, vault RNA, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	166.10 Å
Forward intensity I(0) i0	587828000.00
Molecular weight molecular_weight	207010.0 kDa
Excluded volume excluded_volume	259740 Å³
Envelope volume envelope_volume	1127800 Å³
Hydration-shell volume shell_volume	63081 Å³
Envelope diameter envelope_diameter	667.5 Å
Shell Rg shell_rg	93.39 Å
Envelope Rg envelope_rg	186.50 Å
Shape Rg shape_rg	165.90 Å
Total Rg total_rg	166.30 Å
Total atoms total_atoms	14604
Residues n_residues	1838
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	384.6 Å
Rg (real space) rg_real	137.30 Å
Rg uncertainty (real space) rg_real_error	2.90 Å
I(0) (real space) i0_real	5.4540e+08
I(0) uncertainty (real space) i0_real_error	1.2720e+07
Rg (reciprocal space) rg_reciprocal	103.40 Å
I(0) (reciprocal space) i0_reciprocal	494100000.0000
Solution quality estimate total_estimate	0.6726
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	42.7 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-1.158
Angular range angular_range	— – 0.0450 Å⁻¹
Current regularization parameter α current_alpha	0.1436
Highest regularization parameter α highest_alpha	107600000.0000
Real-space data points n_real_points	10
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.372; Oscil: 0.113; Stabil: 0.946; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.451

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Major vault protein
Molecular weight formula_weight	99452.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	14604

MATEEFIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPMRMVTVPPRHYCTVANPVSRDAQGLVLFDVTGQVRLRHADLEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKDGDKVVAGDEWLFEGPGTYIPRKEVEVVEIIQATIIRQNQALRLRARKECWDRDGKERVTGEEWLVTTVGAYLPAVFEEVLDLVDAVILTEKTALHLRARRNFRDFRGVSRRTGEEWLVTVQDTEAHVPDVHEEVLGVVPITTLGPHNYCVILDPVGPDGKNQLGQKRVVKGEKSFFLQPGEQLEQGIQDVYVLSEQQGLLLRALQPLEEGEDEEKVSHQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPPGVEELLNKGQDPLADRGEKDTAKSLQPLAPRNKTRVVSYRVPHNAAVQVYDYREKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRTAVFGFETSEAKGPDGMALPRPRDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGTAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELQRVQKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEAIGPSTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTAFGLLGMGPEGQPLGRRVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Protein mono-ADP-ribosyltransferase PARP4
Molecular weight formula_weight	192810.2 kDa
EC 编号 ec_number	2.4.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQLNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCPDSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSRDCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQLASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGILLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVCETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRVNETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSDSLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVTTDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQLPDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFPLDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGNLPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTKQSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYLPRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIALHALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYLSLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCGAGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFLNDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGILHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAKEDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSEDFEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILAPAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQSASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFSLPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCLLEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDEIVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGRECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTEGQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG

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	Trichoplusia ni

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8. Citations (4)

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Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	44443

fit	/app/data/saxs_computation/bw/9bw6/9bw6.fit
pddf	/app/data/pr_computation/bw/9bw6/9bw6.pr.out
profile	/app/data/saxs_computation/bw/9bw6/9bw6.dat

Human Vault Cage in complex with PARP4

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

Major vault protein

State in the Current Structure

Other States of the Same Protein in the Database

Protein mono-ADP-ribosyltransferase PARP4

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)