11JB | pdb_000011jb

RNA Vault with ADPR bound (MVP/PARP4/TEP1 NADP sample)

PDB DOI: https://doi.org/10.2210/pdb11JB/pdb
EM Map EMD-75731: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-02-26 Released: 2026-05-20
Deposition Author(s): Osinski, A., Tagliabracci, V.S.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

TIR-like NADases act in bacterial immunity and the RNA vault

Osinski, A., Mayro, B., Lopez, V.A., Schrad, J., Choi, H., Tomchick, D.R., Pawlowski, K., Forsberg, K., Shahmoradian, S.H., Tagliabracci, V.S.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.05.01.722283

Macromolecule Content

Total Structure Weight: 7,800.94 kDa
Atom Count: 481,962
Modeled Residue Count: 60,450
Deposited Residue Count: 69,654
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major vault protein	A AA [auth a] AB [auth 1] B BA [auth b] A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], IB [auth 9], J, JA [auth j], JB [auth 0], K, KA [auth k], KB [auth AA], L, LA [auth l], LB [auth AB], M, MA [auth m], MB [auth AC], N, NA [auth n], NB [auth AD], O, OA [auth o], OB [auth AE], P, PA [auth p], PB [auth AF], Q, QA [auth q], QB [auth AG], R, RA [auth r], RB [auth AH], S, SA [auth s], SB [auth AI], T, TA [auth t], TB [auth AJ], U, UA [auth u], UB [auth AK], V, VA [auth v], VB [auth AL], W, WA [auth w], WB [auth AM], X, XA [auth x], XB [auth AN], Y, YA [auth y], YB [auth AO], Z, ZA [auth z], ZB [auth AP]	893	Homo sapiens	Mutation(s): 0 Gene Names: MVP, LRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14764 (Homo sapiens) Explore Q14764 Go to UniProtKB: Q14764
PHAROS: Q14764 GTEx: ENSG00000013364
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14764
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 (Subject of Investigation/LOI) Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain AC [auth A] SDF format, chain AD [auth a] SDF format, chain AE [auth 1] SDF format, chain BC [auth B] SDF format, chain BD [auth b] SDF format, chain BE [auth 2] SDF format, chain CC [auth C] SDF format, chain CD [auth c] SDF format, chain CE [auth 3] SDF format, chain DC [auth D] SDF format, chain DD [auth d] SDF format, chain DE [auth 4] SDF format, chain EC [auth E] SDF format, chain ED [auth e] SDF format, chain EE [auth 5] SDF format, chain FC [auth F] SDF format, chain FD [auth f] SDF format, chain GC [auth G] SDF format, chain GD [auth g] SDF format, chain GE [auth 7] SDF format, chain HC [auth H] SDF format, chain HD [auth h] SDF format, chain IC [auth I] SDF format, chain ID [auth i] SDF format, chain IE [auth 9] SDF format, chain JC [auth J] SDF format, chain JD [auth j] SDF format, chain JE [auth 0] SDF format, chain KC [auth K] SDF format, chain KD [auth k] SDF format, chain KE [auth AA] SDF format, chain LC [auth L] SDF format, chain LD [auth l] SDF format, chain LE [auth AB] SDF format, chain MC [auth M] SDF format, chain MD [auth m] SDF format, chain ME [auth AC] SDF format, chain NC [auth N] SDF format, chain ND [auth n] SDF format, chain NE [auth AD] SDF format, chain OC [auth O] SDF format, chain OD [auth o] SDF format, chain OE [auth AE] SDF format, chain PC [auth P] SDF format, chain PD [auth p] SDF format, chain PE [auth AF] SDF format, chain QD [auth q] SDF format, chain QE [auth AG] SDF format, chain RC [auth R] SDF format, chain RD [auth r] SDF format, chain RE [auth AH] SDF format, chain SC [auth S] SDF format, chain SD [auth s] SDF format, chain SE [auth AI] SDF format, chain TC [auth T] SDF format, chain TD [auth t] SDF format, chain TE [auth AJ] SDF format, chain UC [auth U] SDF format, chain UD [auth u] SDF format, chain UE [auth AK] SDF format, chain VC [auth V] SDF format, chain VD [auth v] SDF format, chain VE [auth AL] SDF format, chain WC [auth W] SDF format, chain WD [auth w] SDF format, chain WE [auth AM] SDF format, chain XC [auth X] SDF format, chain XD [auth x] SDF format, chain XE [auth AN] SDF format, chain YC [auth Y] SDF format, chain YD [auth y] SDF format, chain YE [auth AO] SDF format, chain ZC [auth Z] SDF format, chain ZD [auth z] SDF format, chain ZE [auth AP] SDF format, chain QC [auth Q] SDF format, chain HE [auth 8] SDF format, chain FE [auth 6] MOL2 format, chain AC [auth A] MOL2 format, chain AD [auth a] MOL2 format, chain AE [auth 1] MOL2 format, chain BC [auth B] MOL2 format, chain BD [auth b] MOL2 format, chain BE [auth 2] MOL2 format, chain CC [auth C] MOL2 format, chain CD [auth c] MOL2 format, chain CE [auth 3] MOL2 format, chain DC [auth D] MOL2 format, chain DD [auth d] MOL2 format, chain DE [auth 4] MOL2 format, chain EC [auth E] MOL2 format, chain ED [auth e] MOL2 format, chain EE [auth 5] MOL2 format, chain FC [auth F] MOL2 format, chain FD [auth f] MOL2 format, chain GC [auth G] MOL2 format, chain GD [auth g] MOL2 format, chain GE [auth 7] MOL2 format, chain HC [auth H] MOL2 format, chain HD [auth h] MOL2 format, chain IC [auth I] MOL2 format, chain ID [auth i] MOL2 format, chain IE [auth 9] MOL2 format, chain JC [auth J] MOL2 format, chain JD [auth j] MOL2 format, chain JE [auth 0] MOL2 format, chain KC [auth K] MOL2 format, chain KD [auth k] MOL2 format, chain KE [auth AA] MOL2 format, chain LC [auth L] MOL2 format, chain LD [auth l] MOL2 format, chain LE [auth AB] MOL2 format, chain MC [auth M] MOL2 format, chain MD [auth m] MOL2 format, chain ME [auth AC] MOL2 format, chain NC [auth N] MOL2 format, chain ND [auth n] MOL2 format, chain NE [auth AD] MOL2 format, chain OC [auth O] MOL2 format, chain OD [auth o] MOL2 format, chain OE [auth AE] MOL2 format, chain PC [auth P] MOL2 format, chain PD [auth p] MOL2 format, chain PE [auth AF] MOL2 format, chain QD [auth q] MOL2 format, chain QE [auth AG] MOL2 format, chain RC [auth R] MOL2 format, chain RD [auth r] MOL2 format, chain RE [auth AH] MOL2 format, chain SC [auth S] MOL2 format, chain SD [auth s] MOL2 format, chain SE [auth AI] MOL2 format, chain TC [auth T] MOL2 format, chain TD [auth t] MOL2 format, chain TE [auth AJ] MOL2 format, chain UC [auth U] MOL2 format, chain UD [auth u] MOL2 format, chain UE [auth AK] MOL2 format, chain VC [auth V] MOL2 format, chain VD [auth v] MOL2 format, chain VE [auth AL] MOL2 format, chain WC [auth W] MOL2 format, chain WD [auth w] MOL2 format, chain WE [auth AM] MOL2 format, chain XC [auth X] MOL2 format, chain XD [auth x] MOL2 format, chain XE [auth AN] MOL2 format, chain YC [auth Y] MOL2 format, chain YD [auth y] MOL2 format, chain YE [auth AO] MOL2 format, chain ZC [auth Z] MOL2 format, chain ZD [auth z] MOL2 format, chain ZE [auth AP] MOL2 format, chain QC [auth Q] MOL2 format, chain HE [auth 8] MOL2 format, chain FE [auth 6] mmCIF format, chain AC [auth A] mmCIF format, chain AD [auth a] mmCIF format, chain AE [auth 1] mmCIF format, chain BC [auth B] mmCIF format, chain BD [auth b] mmCIF format, chain BE [auth 2] mmCIF format, chain CC [auth C] mmCIF format, chain CD [auth c] mmCIF format, chain CE [auth 3] mmCIF format, chain DC [auth D] mmCIF format, chain DD [auth d] mmCIF format, chain DE [auth 4] mmCIF format, chain EC [auth E] mmCIF format, chain ED [auth e] mmCIF format, chain EE [auth 5] mmCIF format, chain FC [auth F] mmCIF format, chain FD [auth f] mmCIF format, chain GC [auth G] mmCIF format, chain GD [auth g] mmCIF format, chain GE [auth 7] mmCIF format, chain HC [auth H] mmCIF format, chain HD [auth h] mmCIF format, chain IC [auth I] mmCIF format, chain ID [auth i] mmCIF format, chain IE [auth 9] mmCIF format, chain JC [auth J] mmCIF format, chain JD [auth j] mmCIF format, chain JE [auth 0] mmCIF format, chain KC [auth K] mmCIF format, chain KD [auth k] mmCIF format, chain KE [auth AA] mmCIF format, chain LC [auth L] mmCIF format, chain LD [auth l] mmCIF format, chain LE [auth AB] mmCIF format, chain MC [auth M] mmCIF format, chain MD [auth m] mmCIF format, chain ME [auth AC] mmCIF format, chain NC [auth N] mmCIF format, chain ND [auth n] mmCIF format, chain NE [auth AD] mmCIF format, chain OC [auth O] mmCIF format, chain OD [auth o] mmCIF format, chain OE [auth AE] mmCIF format, chain PC [auth P] mmCIF format, chain PD [auth p] mmCIF format, chain PE [auth AF] mmCIF format, chain QD [auth q] mmCIF format, chain QE [auth AG] mmCIF format, chain RC [auth R] mmCIF format, chain RD [auth r] mmCIF format, chain RE [auth AH] mmCIF format, chain SC [auth S] mmCIF format, chain SD [auth s] mmCIF format, chain SE [auth AI] mmCIF format, chain TC [auth T] mmCIF format, chain TD [auth t] mmCIF format, chain TE [auth AJ] mmCIF format, chain UC [auth U] mmCIF format, chain UD [auth u] mmCIF format, chain UE [auth AK] mmCIF format, chain VC [auth V] mmCIF format, chain VD [auth v] mmCIF format, chain VE [auth AL] mmCIF format, chain WC [auth W] mmCIF format, chain WD [auth w] mmCIF format, chain WE [auth AM] mmCIF format, chain XC [auth X] mmCIF format, chain XD [auth x] mmCIF format, chain XE [auth AN] mmCIF format, chain YC [auth Y] mmCIF format, chain YD [auth y] mmCIF format, chain YE [auth AO] mmCIF format, chain ZC [auth Z] mmCIF format, chain ZD [auth z] mmCIF format, chain ZE [auth AP] mmCIF format, chain QC [auth Q] mmCIF format, chain HE [auth 8] mmCIF format, chain FE [auth 6]	AC [auth A] AD [auth a] AE [auth 1] BC [auth B] BD [auth b] AC [auth A], AD [auth a], AE [auth 1], BC [auth B], BD [auth b], BE [auth 2], CC [auth C], CD [auth c], CE [auth 3], DC [auth D], DD [auth d], DE [auth 4], EC [auth E], ED [auth e], EE [auth 5], FC [auth F], FD [auth f], FE [auth 6], GC [auth G], GD [auth g], GE [auth 7], HC [auth H], HD [auth h], HE [auth 8], IC [auth I], ID [auth i], IE [auth 9], JC [auth J], JD [auth j], JE [auth 0], KC [auth K], KD [auth k], KE [auth AA], LC [auth L], LD [auth l], LE [auth AB], MC [auth M], MD [auth m], ME [auth AC], NC [auth N], ND [auth n], NE [auth AD], OC [auth O], OD [auth o], OE [auth AE], PC [auth P], PD [auth p], PE [auth AF], QC [auth Q], QD [auth q], QE [auth AG], RC [auth R], RD [auth r], RE [auth AH], SC [auth S], SD [auth s], SE [auth AI], TC [auth T], TD [auth t], TE [auth AJ], UC [auth U], UD [auth u], UE [auth AK], VC [auth V], VD [auth v], VE [auth AL], WC [auth W], WD [auth w], WE [auth AM], XC [auth X], XD [auth x], XE [auth AN], YC [auth Y], YD [auth y], YE [auth AO], ZC [auth Z], ZD [auth z], ZE [auth AP]	[(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 C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain AC [auth A] Focus chain AD [auth a] Focus chain AE [auth 1] Focus chain BC [auth B] Focus chain BD [auth b] Focus chain BE [auth 2] Focus chain CC [auth C] Focus chain CD [auth c] Focus chain CE [auth 3] Focus chain DC [auth D] Focus chain DD [auth d] Focus chain DE [auth 4] Focus chain EC [auth E] Focus chain ED [auth e] Focus chain EE [auth 5] Focus chain FC [auth F] Focus chain FD [auth f] Focus chain FE [auth 6] Focus chain GC [auth G] Focus chain GD [auth g] Focus chain GE [auth 7] Focus chain HC [auth H] Focus chain HD [auth h] Focus chain HE [auth 8] Focus chain IC [auth I] Focus chain ID [auth i] Focus chain IE [auth 9] Focus chain JC [auth J] Focus chain JD [auth j] Focus chain JE [auth 0] Focus chain KC [auth K] Focus chain KD [auth k] Focus chain KE [auth AA] Focus chain LC [auth L] Focus chain LD [auth l] Focus chain LE [auth AB] Focus chain MC [auth M] Focus chain MD [auth m] Focus chain ME [auth AC] Focus chain NC [auth N] Focus chain ND [auth n] Focus chain NE [auth AD] Focus chain OC [auth O] Focus chain OD [auth o] Focus chain OE [auth AE] Focus chain PC [auth P] Focus chain PD [auth p] Focus chain PE [auth AF] Focus chain QC [auth Q] Focus chain QD [auth q] Focus chain QE [auth AG] Focus chain RC [auth R] Focus chain RD [auth r] Focus chain RE [auth AH] Focus chain SC [auth S] Focus chain SD [auth s] Focus chain SE [auth AI] Focus chain TC [auth T] Focus chain TD [auth t] Focus chain TE [auth AJ] Focus chain UC [auth U] Focus chain UD [auth u] Focus chain UE [auth AK] Focus chain VC [auth V] Focus chain VD [auth v] Focus chain VE [auth AL] Focus chain WC [auth W] Focus chain WD [auth w] Focus chain WE [auth AM] Focus chain XC [auth X] Focus chain XD [auth x] Focus chain XE [auth AN] Focus chain YC [auth Y] Focus chain YD [auth y] Focus chain YE [auth AO] Focus chain ZC [auth Z] Focus chain ZD [auth z] Focus chain ZE [auth AP] Interactions & Density Focus chain AC [auth A] Focus chain AD [auth a] Focus chain AE [auth 1] Focus chain BC [auth B] Focus chain BD [auth b] Focus chain BE [auth 2] Focus chain CC [auth C] Focus chain CD [auth c] Focus chain CE [auth 3] Focus chain DC [auth D] Focus chain DD [auth d] Focus chain DE [auth 4] Focus chain EC [auth E] Focus chain ED [auth e] Focus chain EE [auth 5] Focus chain FC [auth F] Focus chain FD [auth f] Focus chain FE [auth 6] Focus chain GC [auth G] Focus chain GD [auth g] Focus chain GE [auth 7] Focus chain HC [auth H] Focus chain HD [auth h] Focus chain HE [auth 8] Focus chain IC [auth I] Focus chain ID [auth i] Focus chain IE [auth 9] Focus chain JC [auth J] Focus chain JD [auth j] Focus chain JE [auth 0] Focus chain KC [auth K] Focus chain KD [auth k] Focus chain KE [auth AA] Focus chain LC [auth L] Focus chain LD [auth l] Focus chain LE [auth AB] Focus chain MC [auth M] Focus chain MD [auth m] Focus chain ME [auth AC] Focus chain NC [auth N] Focus chain ND [auth n] Focus chain NE [auth AD] Focus chain OC [auth O] Focus chain OD [auth o] Focus chain OE [auth AE] Focus chain PC [auth P] Focus chain PD [auth p] Focus chain PE [auth AF] Focus chain QC [auth Q] Focus chain QD [auth q] Focus chain QE [auth AG] Focus chain RC [auth R] Focus chain RD [auth r] Focus chain RE [auth AH] Focus chain SC [auth S] Focus chain SD [auth s] Focus chain SE [auth AI] Focus chain TC [auth T] Focus chain TD [auth t] Focus chain TE [auth AJ] Focus chain UC [auth U] Focus chain UD [auth u] Focus chain UE [auth AK] Focus chain VC [auth V] Focus chain VD [auth v] Focus chain VE [auth AL] Focus chain WC [auth W] Focus chain WD [auth w] Focus chain WE [auth AM] Focus chain XC [auth X] Focus chain XD [auth x] Focus chain XE [auth AN] Focus chain YC [auth Y] Focus chain YD [auth y] Focus chain YE [auth AO] Focus chain ZC [auth Z] Focus chain ZD [auth z] Focus chain ZE [auth AP]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Osinski, A.

Tagliabracci, V.S.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM137419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM158265
Welch Foundation	United States	I-1911
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR150033