9RCV | pdb_00009rcv

Structure of the Human Peptide-Loading Complex Arrested by HCMV US6

PDB DOI: https://doi.org/10.2210/pdb9RCV/pdb
EM Map EMD-53923: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-05-29 Released: 2025-12-03
Deposition Author(s): Stolz, M., Susac, L., Trowitzsch, S., Tampe, R.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 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

US6 hijacks peptide-loading complex by trapping transporter-chaperone dynamics

Stolz, M., Susac, L., Trowitzsch, S., Tampe, R.

To be published.

Macromolecule Content

Total Structure Weight: 382.5 kDa
Atom Count: 23,529
Modeled Residue Count: 2,993
Deposited Residue Count: 3,466
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen peptide transporter 1	A	748	Homo sapiens	Mutation(s): 1 EC: 7.4.2.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q03518 (Homo sapiens) Explore Q03518 Go to UniProtKB: Q03518
PHAROS: Q03518 GTEx: ENSG00000168394
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03518
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tapasin	B, F	448	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for O15533 (Homo sapiens) Explore O15533 Go to UniProtKB: O15533
PHAROS: O15533 GTEx: ENSG00000231925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15533
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain F	Go to GlyGen: O15533-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	C, G	362	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A678ZHF8 (Homo sapiens) Explore A0A678ZHF8 Go to UniProtKB: A0A678ZHF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A678ZHF8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain G
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D, H	119	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen peptide transporter 2	E	677	Homo sapiens	Mutation(s): 0 EC: 7.4.2.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q03519 (Homo sapiens) Explore Q03519 Go to UniProtKB: Q03519
PHAROS: Q03519 GTEx: ENSG00000204267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03519
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Unique short US6 glycoprotein	I	183	Homo sapiens	Mutation(s): 0 Gene Names: US6
UniProt
Find proteins for P14334 (Human cytomegalovirus (strain AD169)) Explore P14334 Go to UniProtKB: P14334
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14334
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	2		N-Glycosylation	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E] mmCIF format, chain O [auth E]	O [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth G] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth G] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth G]	N [auth C], Q [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Focus chain Q [auth G] Interactions & Density Focus chain N [auth C] Focus chain Q [auth G]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth E] MOL2 format, chain M [auth A] MOL2 format, chain P [auth E] mmCIF format, chain M [auth A] mmCIF format, chain P [auth E]	M [auth A], P [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth E] Interactions & Density Focus chain M [auth A] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	789121
European Research Council (ERC)	European Union	101141396
German Research Foundation (DFG)	Germany	TA157/12-1
German Research Foundation (DFG)	Germany	CRC1507/P18
Other private	United States	UR013222