5m3l

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin

Method: ELECTRON MICROSCOPY

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

Extracellular globin-4

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-2 × 3 （P02218） Extracellular globin-3 × 3 （P11069） Hemoglobin chain d1 × 3 （O61233） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB4_LUMTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 1–151 Author chain E； PDBConstruct 1–151； UniProt 1–151 Author chain I； PDBConstruct 1–151； UniProt 1–151

Extracellular globin-2

OrganismNot specified

UniProt P02218

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-3 × 3 （P11069） Hemoglobin chain d1 × 3 （O61233） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB2_LUMTE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–145； UniProt 1–145 Author chain F； PDBConstruct 1–145； UniProt 1–145 Author chain J； PDBConstruct 1–145； UniProt 1–145

Extracellular globin-3

OrganismNot specified

UniProt P11069

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-2 × 3 （P02218） Hemoglobin chain d1 × 3 （O61233） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB3_LUMTE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–153； UniProt 18–170 Author chain G； PDBConstruct 1–153； UniProt 18–170 Author chain K； PDBConstruct 1–153； UniProt 18–170

Hemoglobin chain d1

OrganismNot specified

UniProt O61233

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-2 × 3 （P02218） Extracellular globin-3 × 3 （P11069） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O61233_LUMTE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–140； UniProt 19–158 Author chain H； PDBConstruct 1–140； UniProt 19–158 Author chain L； PDBConstruct 1–140； UniProt 19–158

Hemoglobin linker chain L1

OrganismNot specified

UniProt Q9GV76

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-2 × 3 （P02218） Extracellular globin-3 × 3 （P11069） Hemoglobin chain d1 × 3 （O61233） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9GV76_LUMTE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–217； UniProt 24–240

Extracellular hemoglobin linker L2 subunit

OrganismNot specified

UniProt Q2I743

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-2 × 3 （P02218） Extracellular globin-3 × 3 （P11069） Hemoglobin chain d1 × 3 （O61233） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L3 subunit × 1 （Q2I742） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2I743_LUMTE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–220； UniProt 47–266

Extracellular hemoglobin linker L3 subunit

OrganismNot specified

UniProt Q2I742

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	Extracellular globin-4 × 3 （P13579） Extracellular globin-2 × 3 （P02218） Extracellular globin-3 × 3 （P11069） Hemoglobin chain d1 × 3 （O61233） Hemoglobin linker chain L1 × 1 （Q9GV76） Extracellular hemoglobin linker L2 subunit × 1 （Q2I743） PROTOPORPHYRIN IX CONTAINING FE × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2I742_LUMTE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain O； PDBConstruct 1–215； UniProt 26–240

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	5m3l
Deposition date deposition_date	2016-10-15
Structure title title	Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin
Keywords keywords	Lumbricus terrestris, hemoglobin, oxygen carrier, erythrocruorin, oxygen transport; OXYGEN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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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.

5m3l__assembly_1__model_1

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

Download this curve (.dat)

5m3l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m3l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.65 Å
Rg (electron density)	43.17 Å
Total Rg	43.59 Å
Atom count	19007
Residues	2394
Excluded volume	337040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m3l__assembly_1__model_1`	pentadecameric （15）	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 (8)

Entity 1 Entity 1 polymer

Description description	Extracellular globin-4
Molecular weight formula_weight	17567.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	19007

ADDEDCCSYEDRREIRHIWDDVWSSSFTDRRVAIVRAVFDDLFKHYPTSKALFERVKIDEPESGEFKSHLVRVANGLKLLINLLDDTLVLQSHLGHLADQHIQRKGVTKEYFRGIGEAFARVLPQVLSCFNVDAWNRCFHRLVARIAKDLP

Entity 2 Entity 2 polymer

Description description	Extracellular globin-2
Molecular weight formula_weight	16268.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

KKQCGVLEGLKVKSEWGRAYGSGHDREAFSQAIWRATFAQVPESRSLFKRVHGDDTSHPAFIAHADRVLGGLDIAISTLDQPATLKEELDHLQVQHEGRKIPDNYFDAFKTAILHVVAAQLGRCYDREAWDACIDHIEDGIKGHH

Entity 3 Entity 3 polymer

Description description	Extracellular globin-3
Molecular weight formula_weight	17331.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

DEHEHCCSEEDHRIVQKQWDILWRDTESSKIKIGFGRLLLTKLAKDIPEVNDLFKRVDIEHAEGPKFSAHALRILNGLDLAINLLDDPPALDAALDHLAHQHEVREGVQKAHFKKFGEILATGLPQVLDDYDALAWKSCLKGILTKISSRLNA

Entity 4 Entity 4 polymer

Description description	Hemoglobin chain d1
Molecular weight formula_weight	15988.3 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

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

ECLVTESLKVKLQWASAFGHAHERVAFGLELWRDIIDDHPEIKAPFSRVRGDNIYSPEFGAHSQRVLSGLDITISMLDTPDMLAAQLAHLKVQHVERNLKPEFFDIFLKHLLHVLGDRLGTHFDFGAWHDCVDQIIDGIK

Entity 5 Entity 5 polymer

Description description	Hemoglobin linker chain L1
Molecular weight formula_weight	24936.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

RFQYLVKNQNLHIDYLAKKLHDIEEEYNKLTHDVDKKTIRQLKARISNLEEHHCDEHESECRGDVPECIHDLLFCDGEKDCRDGSDEDPETCSLNITHVGSSYTGLATWTSCEDLNPDHAIVTITAAHRKSFFPNRVWLRATLSYELDEHDHTVSTTQLRGFYNFGKRELLLAPLKGQSEGYGVICDFNLGDDDHADCKIVVPSSLFVCAHFNAQRY

Entity 6 Entity 6 polymer

Description description	Extracellular hemoglobin linker L2 subunit
Molecular weight formula_weight	25085.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

LDPRLGANAFLIIRLDRIIEKLRTKLDEAEKIDPEHFVSEIDARVEKIEGTHCEKRTFQCGGNEQECISDLLVCDGHKDCHNAHDEDPDVCDTSVVKAGNVFSGTSTWHGCLAREDHVTRITITASKRRKFFTARIWLRALVESELERHGENVTSSFNAKGYYNFASRRLILLPTDDHDDHLAVVCSFNRGDNERAECHRVTEATLHQCADLFVTLEEHD

Entity 7 Entity 7 polymer

Description description	Extracellular hemoglobin linker L3 subunit
Molecular weight formula_weight	24486.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

QSHDEIIDKIIERTNKITTSISHVESLLDDRLDPKRIRKAGSLRHRVEELEDPSCDEHEHQCGGDDPQCISKLFVCDGHNDCRNGEDEKDCTLPTKAGDKFIGDVCFDHCTKRRPEHMTLAFESSSIAAFFTPIADLHVHIEIESETDEDESEVSMPADGEYSFADHRLTIHPPEEDGLGLVGEFDGYNFDRFVGHIVHELSEEVCAEFIFHRKK

Entity 8 Entity 8 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	5m3lA00
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	5m3lB00
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	5m3lC00
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	5m3lD00
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	5m3lE00
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	5m3lF00
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	5m3lG00
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	5m3lH00
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	5m3lI00
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	5m3lJ00
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	5m3lK00
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	5m3lL00
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	5m3lM01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1520 —

Domain ID domain_id	5m3lM02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	5m3lN01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1530 —

Domain ID domain_id	5m3lN02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	5m3lO01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	5m3lO02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	620 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	146.670 Å
R factor r_factor	0.3310
R_work r_work	0.3309
R_free r_free	0.3323

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	75000

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin

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

Extracellular globin-4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Extracellular globin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Extracellular globin-3

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 chain d1

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 linker chain L1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Extracellular hemoglobin linker L2 subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Extracellular hemoglobin linker L3 subunit

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

5m3l__assembly_1__model_1

5m3l__assembly_1__model_1 | I(q)

5m3l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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 polymer

Polymer Polymer

Entity 6 Entity 6 polymer