SAXSdb — 2ol3

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1. Protein Identity and Related Structures Protein Identity & Related Structures

BM3.3 T-CELL RECEPTOR ALPHA-CHAIN

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BM3.3 T-CELL RECEPTOR BETA-CHAIN × 1 （P04214） ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE × 1 （P01901） Beta-2-microglobulin × 1 （P01887） NATURALLY PROCESSED OCTAPEPTIDE PBM8 × 1 （Q91YE7） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5R1F1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 23–116

BM3.3 T-CELL RECEPTOR BETA-CHAIN

Mus musculus

UniProt P04214

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BM3.3 T-CELL RECEPTOR ALPHA-CHAIN × 1 （Q5R1F1） ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE × 1 （P01901） Beta-2-microglobulin × 1 （P01887） NATURALLY PROCESSED OCTAPEPTIDE PBM8 × 1 （Q91YE7） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVB6_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 22–116

ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE

Mus musculus

UniProt P01901

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BM3.3 T-CELL RECEPTOR ALPHA-CHAIN × 1 （Q5R1F1） BM3.3 T-CELL RECEPTOR BETA-CHAIN × 1 （P04214） Beta-2-microglobulin × 1 （P01887） NATURALLY PROCESSED OCTAPEPTIDE PBM8 × 1 （Q91YE7） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA1B_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–279； UniProt 22–300

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BM3.3 T-CELL RECEPTOR ALPHA-CHAIN × 1 （Q5R1F1） BM3.3 T-CELL RECEPTOR BETA-CHAIN × 1 （P04214） ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE × 1 （P01901） NATURALLY PROCESSED OCTAPEPTIDE PBM8 × 1 （Q91YE7） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain L； PDBConstruct 2–100； UniProt 21–119

NATURALLY PROCESSED OCTAPEPTIDE PBM8

OrganismNot specified

UniProt Q91YE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BM3.3 T-CELL RECEPTOR ALPHA-CHAIN × 1 （Q5R1F1） BM3.3 T-CELL RECEPTOR BETA-CHAIN × 1 （P04214） ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE × 1 （P01901） Beta-2-microglobulin × 1 （P01887） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBM5_MOUSE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain P； PDBConstruct 1–8； UniProt 484–491

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_id	2ol3
Deposition date deposition_date	2007-01-18
Structure title title	crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule
Keywords keywords	T CELL RECEPTOR, CLASS I MHC, H-2KBm8, TCR-PMHC COMPLEX, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-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.

2ol3__assembly_1__model_1

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

Download this curve (.dat)

2ol3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ol3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.08 Å
Rg (electron density)	31.23 Å
Total Rg	31.76 Å
Atom count	4996
Residues	615
Excluded volume	88424 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ol3__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	BM3.3 T-CELL RECEPTOR ALPHA-CHAIN
Molecular weight formula_weight	15570.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5073

QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATVGHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKPGSADDAKKDAAKKDDAKKDAAKKDGS

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	BM3.3 T-CELL RECEPTOR BETA-CHAIN
Molecular weight formula_weight	13065.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIVV

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE
Molecular weight formula_weight	32078.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GPHSLRYFVTAVSRPGLGEPRFISVGYVDNTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPPPS

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11835.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	NATURALLY PROCESSED OCTAPEPTIDE PBM8
Molecular weight formula_weight	1037.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

SQYYYNSL

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2ol3a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ol3b_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ol3h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2ol3h2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d2ol3l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2ol3l3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	2ol3A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ol3B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ol3H01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	2ol3H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ol3L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	102.523 Å
Unit-cell length b length_b	102.523 Å
Unit-cell length c length_c	198.381 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2272
R_work r_work	0.2242
R_free r_free	0.2835

crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule

1. Protein Identity and Related Structures Protein Identity & Related Structures

BM3.3 T-CELL RECEPTOR ALPHA-CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

BM3.3 T-CELL RECEPTOR BETA-CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ALLOGENEIC H-2KBM8 MHC CLASS I MOLECULE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NATURALLY PROCESSED OCTAPEPTIDE PBM8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ol3__assembly_1__model_1

2ol3__assembly_1__model_1 | I(q)

2ol3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)