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5wer

Crystal Structure of TAPBPR and H2-Dd complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

H-2 class I histocompatibility antigen, D-D alpha chain

Mus musculus

UniProt P01900

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P61769） TAP binding protein related × 1 1,2-ETHANEDIOL × 1 GLYCEROL × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P61769） TAP binding protein related × 1 1,2-ETHANEDIOL × 1 GLYCEROL × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P61769） TAP binding protein related × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P61769） TAP binding protein related × 1 GLYCEROL × 1 PENTAETHYLENE GLYCOL × 1 CITRIC ACID × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bii 1ddh 1qo3 1qo3 3dmm 3e6f 3e6h 3ecb 5ivx 5kd4 5kd4 5kd7

38 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HA12_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–277； UniProt 26–301 Author chain D； PDBConstruct 2–277； UniProt 26–301 Author chain G； PDBConstruct 2–277； UniProt 26–301 Author chain J； PDBConstruct 2–277； UniProt 26–301

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） TAP binding protein related × 1 1,2-ETHANEDIOL × 1 GLYCEROL × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） TAP binding protein related × 1 1,2-ETHANEDIOL × 1 GLYCEROL × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） TAP binding protein related × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-D alpha chain × 1 （P01900） TAP binding protein related × 1 GLYCEROL × 1 PENTAETHYLENE GLYCOL × 1 CITRIC ACID × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1jnj 1lds 1py4 1py4 1py4 1py4 2d4d 2d4f 2vb5 2xks 2xku 2yxf

61 assemblies; showing the first 12

Homodimer
2x89 2x89 2z9t 3low 4r9h 4r9h 4ra3 4ra3 4rah 6m1b

10 assemblies

Homotetramer
2e8d 2f8o 3tlr 3tm6 3tm6 7afv

6 assemblies

Other homooligomers
3ciq 3ciq 3loz 6gk3 8a7o 8a7p 8a7q 8a7t

8 assemblies

Heteromeric or nucleic-acid complex
1a1m 1a1n 1a1o 1a6z 1a6z 1a9b 1a9b 1a9e 1agb 1agc 1agd 1age

1914 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–100； UniProt 21–119 Author chain E； PDBConstruct 2–100； UniProt 21–119 Author chain H； PDBConstruct 2–100； UniProt 21–119 Author chain K； PDBConstruct 2–100； UniProt 21–119

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_id5wer
Deposition date deposition_date2017-07-10
Structure title titleCrystal Structure of TAPBPR and H2-Dd complex
Keywords keywords;Antigen presentation, peptide editing, MAJOR HISTOMPATIBILITY COMPLEX CLASS I, MHC-I, TAPASIN, Peptide Loading Complex, PLC, IMMUNE RESPONSE, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5wer__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5wer__assembly_2__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5wer__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）29.51 Å
Rg (electron density)28.66 Å
Total Rg29.37 Å
Atom count4936
Residues678
Excluded volume86228 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5wer__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5wer__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5wer__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5wer__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5werA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5werA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5werD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5werG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werJ01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5werJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5werK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)