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3e3q

Structure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9

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

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

Mus musculus

UniProt P01897

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 4 QL9 peptide × 1 T-cell receptor alpha chain V region PHDS58 × 1 （P01738） TCR beta chain × 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
1ld9 1ld9 1ldp 2e7l 2e7l 2oi9 3e2h 3e3q 3e3q 3e3q 3e3q 3e3q

33 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HA1L_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–175； UniProt 25–199 Author chain B； PDBConstruct 1–175； UniProt 25–199 Author chain H； PDBConstruct 1–175； UniProt 25–199 Author chain L； PDBConstruct 1–175； UniProt 25–199 Author chain P； PDBConstruct 1–175； UniProt 25–199 Author chain U； PDBConstruct 1–175； UniProt 25–199 Author chain Y； PDBConstruct 1–175； UniProt 25–199 Author chain c； PDBConstruct 1–175； UniProt 25–199

T-cell receptor alpha chain V region PHDS58

Mus musculus

UniProt P01738

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 4 H-2 class I histocompatibility antigen, L-D alpha chain × 1 （P01897） QL9 peptide × 1 TCR beta chain × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1i9e

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1g6r 1g6r 2icw 2icw 2oi9 3e2h 3e3q 3e3q 3e3q 3e3q 3e3q 3e3q

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TVA1_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–109； UniProt 22–130 Author chain D； PDBConstruct 1–109； UniProt 22–130 Author chain I； PDBConstruct 1–109； UniProt 22–130 Author chain M； PDBConstruct 1–109； UniProt 22–130 Author chain R； PDBConstruct 1–109； UniProt 22–130 Author chain V； PDBConstruct 1–109； UniProt 22–130 Author chain Z； PDBConstruct 1–109； UniProt 22–130 Author chain d； PDBConstruct 1–109； UniProt 22–130

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_id3e3q
Deposition date deposition_date2008-08-07
Structure title titleStructure of the 3alpham13 high-affinity mutant of the 2C TCR in complex with Ld/QL9
Keywords keywords;TCR, MHC, high affinity, cross reactivity, Glycoprotein, Immune response, Membrane, MHC I, Phosphoprotein, Transmembrane, Immunoglobulin domain, Receptor, 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.

3e3q__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3e3q__assembly_7__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3e3q__assembly_7__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）23.09 Å
Rg (electron density)22.03 Å
Total Rg23.03 Å
Atom count3226
Residues404
Excluded volume56500 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3e3q__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3e3q__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3e3q__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3e3q__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3e3q__assembly_5__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3e3q__assembly_6__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 3e3q__assembly_7__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 3e3q__assembly_8__model_1 tetrameric （4） 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 (4)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3e3qa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qc_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qe_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qf_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qj_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qn_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qs_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3e3qw_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (24 domains)

Domain ID domain_id3e3qA00
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_id3e3qB00
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_id3e3qC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qH00
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_id3e3qI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qL00
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_id3e3qM00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qN00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qP00
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_id3e3qR00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qS00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qU00
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_id3e3qV00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qW00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qY00
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_id3e3qZ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qa00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qc00
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_id3e3qd00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3e3qe00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)