SAXSdb — 9k2i

▼

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

MHC class I antigen

Homo sapiens

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） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P61769） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8WLS4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–276； UniProt 25–299 Author chain F； PDBConstruct 2–276； UniProt 25–299 Author chain K； PDBConstruct 2–276； UniProt 25–299 Author chain P； PDBConstruct 2–276； UniProt 25–299

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	MHC class I antigen × 1 （Q8WLS4） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （Q8WLS4） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （Q8WLS4） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	MHC class I antigen × 1 （Q8WLS4） PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL × 1 T cell receptor 5934 chain beta × 1 T cell receptor5934 chain alpha × 1	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain L； PDBConstruct 2–100； UniProt 21–119 Author chain Q； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9k2i
Deposition date deposition_date	2024-10-17
Structure title title	Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2
Keywords keywords	Rac1, Neoantigen, TCR, HLA-A2, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9k2i__assembly_1__model_1

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

Download this curve (.dat)

9k2i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9k2i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.66 Å
Rg (electron density)	37.89 Å
Total Rg	38.01 Å
Atom count	6678
Residues	829
Excluded volume	117100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9k2i__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9k2i__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9k2i__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9k2i__assembly_4__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	31985.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F,K,P
Atom count atom_count	26756

MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G,L,Q

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL
Molecular weight formula_weight	1012.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H,M,R

FSGEYIPTV

Entity 4 Entity 4 polymer

Description description	T cell receptor 5934 chain beta
Molecular weight formula_weight	28086.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,E,T,O

MDTAVSQTPKYLVTQMGNDKSIKCEQNLGHDTMYWYKQDSKKFLKIMFSYNNKELIINETVPNRFSPKSPDKAHLNLHINSLELGDSAVYFCASSQLAGGPLYNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	T cell receptor5934 chain alpha
Molecular weight formula_weight	22912.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,D,S,N

MGENVEQHPSTLSVQEGDSAVIKCTYSDSASNYFPWYKQELGKGPQLIIDIRSNVGEKKDQRIAVTLNKTAKHFSLHITETQPEDSAVYFCAASRGGAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

▶

Unit-cell length a length_a	112.303 Å
Unit-cell length b length_b	147.504 Å
Unit-cell length c length_c	122.171 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	46.967 Å
R factor r_factor	0.2239
R_work r_work	0.2221
R_free r_free	0.2902

Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2

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

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9k2i__assembly_1__model_1

9k2i__assembly_1__model_1 | I(q)

9k2i__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)

Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2

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

MHC class I antigen

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9k2i__assembly_1__model_1

9k2i__assembly_1__model_1 | I(q)

9k2i__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)