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2f54

Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity

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

HLA class I histocompatibility antigen

Homo sapiens

UniProt P01892

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 4 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
1akj 1ao7 1ao7 1aqd 1aqd 1aqd 1aqd 1b0g 1b0g 1b0r 1bd2 1duy

466 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 25–298 Author chain F； PDBConstruct 1–274； UniProt 25–298

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 5 HLA class I histocompatibility antigen × 1 （P01892） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 4 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 G； PDBConstruct 2–100； UniProt 21–119

Cancer/testis antigen 1B

OrganismNot specified

UniProt P78358

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） T-cell receptor alpha chain × 1 （Q6PIZ8） T-cell receptor beta chain × 1 （Q6NS87） water × 4 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
2f53 2f53 2f54 2f54 2p5e 2p5w 2pye 3kla 3kla 6at5 6rp9 6rp9

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CTG1B_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–9； UniProt 157–165 Author chain H； PDBConstruct 1–9； UniProt 157–165

T-cell receptor alpha chain

Homo sapiens

UniProt Q6PIZ8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor beta chain × 1 （Q6NS87） water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor beta chain × 1 （Q6NS87） water × 4 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
2eyr 2eyr 2eys 2eys 2eyt 2eyt 2eyt 2f53 2f53 2f54 2f54 2p5w

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q6PIZ8_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 21–206； UniProt 42–224 Author chain K； PDBConstruct 21–206； UniProt 42–224

T-cell receptor beta chain

Homo sapiens

UniProt Q6NS87

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 HLA class I histocompatibility antigen × 1 （P01892） Beta-2-microglobulin × 1 （P61769） Cancer/testis antigen 1B × 1 （P78358） T-cell receptor alpha chain × 1 （Q6PIZ8） water × 4 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
2f54 2f54 2pye 2pyf

4 assemblies

View Construct and Data Evidence
UniProt name Q6NS87_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 27–241； UniProt 48–266 Author chain L； PDBConstruct 27–241； UniProt 48–266

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_id2f54
Deposition date deposition_date2005-11-25
Structure title titleDirected evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity
Keywords keywordsT-cell receptor, CDR2, Phage display, wild type sequence, high affinity, NY-ESO-1, 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.

2f54__assembly_1__model_1

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

Download this curve (.dat)

2f54__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2f54__assembly_1__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）37.63 Å
Rg (electron density)37.91 Å
Total Rg38.01 Å
Atom count6610
Residues829
Excluded volume115760 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2f54__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2f54__assembly_2__model_1 pentameric （5） 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 (6)

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd2f54a1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd2f54b2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2f54d1
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_idd2f54d2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54e1
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_idd2f54e2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54f1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54f2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd2f54g2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54g3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2f54k1
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_idd2f54k2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2f54l1
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_idd2f54l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (14 domains)

Domain ID domain_id2f54A01
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_id2f54A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54F01
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_id2f54F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54K01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54K02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2f54L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)