1yhu

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

Method: X-RAY DIFFRACTION

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

hemoglobin A1 chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Giant hemoglobins B chain × 6 （P80592） hemoglobin B1a chain × 6 （Q8IFK2） hemoglobin B2 chain × 6 （Q8IFJ9） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 ZINC ION × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IFK4_RIFPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–128； UniProt 1–115 Author chain E； PDBConstruct 14–128； UniProt 1–115 Author chain I； PDBConstruct 14–128； UniProt 1–115 Author chain M； PDBConstruct 14–128； UniProt 1–115 Author chain Q； PDBConstruct 14–128； UniProt 1–115 Author chain U； PDBConstruct 14–128； UniProt 1–115

Giant hemoglobins B chain

OrganismNot specified

UniProt P80592

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	hemoglobin A1 chain × 6 （Q8IFK4） hemoglobin B1a chain × 6 （Q8IFK2） hemoglobin B2 chain × 6 （Q8IFJ9） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 ZINC ION × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLBB_RIFPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–144； UniProt 1–144 Author chain F； PDBConstruct 1–144； UniProt 1–144 Author chain J； PDBConstruct 1–144； UniProt 1–144 Author chain N； PDBConstruct 1–144； UniProt 1–144 Author chain R； PDBConstruct 1–144； UniProt 1–144 Author chain V； PDBConstruct 1–144； UniProt 1–144

hemoglobin B1a chain

OrganismNot specified

UniProt Q8IFK2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	hemoglobin A1 chain × 6 （Q8IFK4） Giant hemoglobins B chain × 6 （P80592） hemoglobin B2 chain × 6 （Q8IFJ9） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 ZINC ION × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IFK2_RIFPA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 16–133； UniProt 1–118 Author chain G； PDBConstruct 16–133； UniProt 1–118 Author chain K； PDBConstruct 16–133； UniProt 1–118 Author chain O； PDBConstruct 16–133； UniProt 1–118 Author chain S； PDBConstruct 16–133； UniProt 1–118 Author chain W； PDBConstruct 16–133； UniProt 1–118

hemoglobin B2 chain

OrganismNot specified

UniProt Q8IFJ9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	hemoglobin A1 chain × 6 （Q8IFK4） Giant hemoglobins B chain × 6 （P80592） hemoglobin B1a chain × 6 （Q8IFK2） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 ZINC ION × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IFJ9_RIFPA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 16–132； UniProt 1–117 Author chain H； PDBConstruct 16–132； UniProt 1–117 Author chain L； PDBConstruct 16–132； UniProt 1–117 Author chain P； PDBConstruct 16–132； UniProt 1–117 Author chain T； PDBConstruct 16–132； UniProt 1–117 Author chain X； PDBConstruct 16–132； UniProt 1–117

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	1yhu
Deposition date deposition_date	2005-01-10
Structure title title	Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.
Keywords keywords	hemoglobin, globin fold, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/TRANSPORT
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.

1yhu__assembly_1__model_1

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

Download this curve (.dat)

1yhu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yhu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.45 Å
Rg (electron density)	47.57 Å
Total Rg	47.87 Å
Atom count	27804
Residues	3516
Excluded volume	492260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yhu__assembly_1__model_1`	24-meric （24）	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 A1 chain
Molecular weight formula_weight	15795.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M,Q,U
Atom count atom_count	27804

ACAMLERAKVKDEWAKAYGIGAARSKFGDALWRNVFNYAPNARDIFESVNSKDMASPEFKAHIARVLGGLDRVISMLDNQATLDADLAHLKSQHDPRTIDPVNFVVFRKALIATVAGTFGVCFDVPAWQGCYNIIAKGITGSDAA

Entity 2 Entity 2 polymer

Description description	Giant hemoglobins B chain
Molecular weight formula_weight	16158.2 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N,R,V

DYVCGPLQRLKVKRQWAEAYGSGNSREEFGHFIWSHVFQHSPAARDMFKRVRGDNIHTPAFRAHATRVLGGLDMCIALLDDEPVLNTQLAHLAKQHETRGVEAAHYDTVNHAVMMGVENVIGSEVFDQDAWKPCLNVITNGIQG

Entity 3 Entity 3 polymer

Description description	hemoglobin B1a chain
Molecular weight formula_weight	15285.3 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O,S,W

AANCADAAAAIVQAQWEDVWSAAAAAASRVSAGEEVFAALFKMVPAAKNLFTRVNVADINSPEFQGHVVRVMGGLDILINALDDIPTLESMLDHLAGQHAVRDGVTGAGFQLMATVLMESLPQVVEGFNPDAWASCLAGIAAAISSAL

Entity 4 Entity 4 polymer

Description description	hemoglobin B2 chain
Molecular weight formula_weight	16162.3 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P,T,X

AASCTTEDRREMQLMWGNVWSAQFTGRRIAIAQAVFKDLFANVPDAVGLFGAVKGDEVNSNEFKAHCIRVVNGLDSSIGLLSDPATLNEQLSHLATQHKARSGVTKGGFSAIAQSFLRVMPQVASCFNPDAWSRCFNRITTGMTEPLPA

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 6 Entity 6 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d1yhua_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhub_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhud_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhue_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuf_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuh_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhui_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuj_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhul_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhum_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhun_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhup_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuq_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhur_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhut_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuu_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhuv_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

Domain ID domain_id	d1yhux_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.0 — automated matches

CATH v4.4 (24 domains)

Domain ID domain_id	1yhuA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuJ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuM00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuN00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuO00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuP00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuQ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuR00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuS00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuT00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuU00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuV00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuW00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1yhuX00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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Unit-cell length a length_a	195.840 Å
Unit-cell length b length_b	195.840 Å
Unit-cell length c length_c	308.820 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	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2433
R_work r_work	0.2433
R_free r_free	0.2707

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

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

hemoglobin A1 chain

State in the Current Structure

Other States of the Same Protein in the Database

Giant hemoglobins B chain

State in the Current Structure

Other States of the Same Protein in the Database

hemoglobin B1a chain

State in the Current Structure

Other States of the Same Protein in the Database

hemoglobin B2 chain

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

1yhu__assembly_1__model_1

1yhu__assembly_1__model_1 | I(q)

1yhu__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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (18 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.

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

hemoglobin A1 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

Giant hemoglobins B 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

hemoglobin B1a 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

hemoglobin B2 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yhu__assembly_1__model_1

1yhu__assembly_1__model_1 | I(q)

1yhu__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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (18 domains)

CATH v4.4 (24 domains)

7. Citations (1)