9bcj

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae

Method: X-RAY DIFFRACTION

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

Hemoglobin subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hemoglobin subunit beta × 2 （P68871） Membrane protein × 2 （Q6NEE5） PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 6 PHOSPHATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HBA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 2–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hemoglobin subunit alpha × 2 （P69905） Membrane protein × 2 （Q6NEE5） PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 6 PHOSPHATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–146； UniProt 2–147

Membrane protein

Corynebacterium diphtheriae NCTC 13129

UniProt Q6NEE5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hemoglobin subunit alpha × 2 （P69905） Hemoglobin subunit beta × 2 （P68871） PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 6 PHOSPHATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6NEE5_CORDI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–198； UniProt 32–229

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	9bcj
Deposition date deposition_date	2024-04-09
Last revision last_revision	2025-01-08
Structure title title	Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae
Keywords keywords	Complex, Hemoglobin, heme, beta-sandwich, PROTEIN BINDING; PROTEIN BINDING
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.

9bcj__assembly_1__model_1

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

Download this curve (.dat)

9bcj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bcj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.72 Å
Rg (electron density)	31.99 Å
Total Rg	32.53 Å
Atom count	7382
Residues	942
Excluded volume	131620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bcj__assembly_1__model_1`	hexameric （6）	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	Hemoglobin subunit alpha
Molecular weight formula_weight	15150.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3972

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Entity 2 Entity 2 polymer

Description description	Hemoglobin subunit beta
Molecular weight formula_weight	15890.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

Entity 3 Entity 3 polymer

Description description	Membrane protein
Molecular weight formula_weight	21918.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SEEVKNADLYWGFSGSSHHKYDHNGPKFEKAGKGAELTNIDAASAYAETFKKGVFPNNKREKSDILVFHNGEVKTETNHSSYQINWPGEVTMKLGYGDGLVIKDLNLMLKNGNMGELKATVGENSNITLFDVQEYSVSDNTITVTPKIPPCTTGTWKPWHNDLTSKLGSLKSVFFESYTCNNDDIAKKPLPLTVVLNG

Source Source

Source organism organism	Corynebacterium diphtheriae NCTC 13129
NCBI taxonomy ID ncbi_taxonomy_id	257309
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
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	269

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Unit-cell length a length_a	58.925 Å
Unit-cell length b length_b	58.925 Å
Unit-cell length c length_c	286.146 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.691 Å
Low-resolution limit resolution_low	19.600 Å
R factor r_factor	0.1898
R_work r_work	0.1885
R_free r_free	0.2147

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae

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

Hemoglobin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Hemoglobin subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Membrane protein

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

9bcj__assembly_1__model_1

9bcj__assembly_1__model_1 | I(q)

9bcj__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae

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

Hemoglobin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemoglobin subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Membrane protein

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

9bcj__assembly_1__model_1

9bcj__assembly_1__model_1 | I(q)

9bcj__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)