SAXSdb — 4m76

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

Complement C3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Integrin alpha-M × 1 （P11215） NICKEL (II) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–298； UniProt 994–1288

Integrin alpha-M

Homo sapiens

UniProt P11215

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Complement C3 × 1 （P01024） NICKEL (II) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITAM_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–198； UniProt 143–337

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	4m76
Deposition date deposition_date	2013-08-12
Structure title title	Integrin I domain of complement receptor 3 in complex with C3d
Keywords keywords	;integrin, complement receptor, immunity, innate immunity, inflammation, phagocytosis, Mac-1, CD11b/CD18, alphaMbeta2, macrophage, Rossmann fold, I domain, Von Willebrand Factor A (VWA), alpha-alpha barrel, adhesion, cell adhesion ;; CELL ADHESION
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.

4m76__assembly_1__model_1

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

Download this curve (.dat)

4m76__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m76__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.33 Å
Rg (electron density)	26.90 Å
Total Rg	27.58 Å
Atom count	3771
Residues	475
Excluded volume	67555 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m76__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Complement C3
Molecular weight formula_weight	33199.0 kDa
Mutation mutation	C1010A, C144A, I332G
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	3804

GAMAVDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD

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

Entity 2 Entity 2 polymer

Description description	Integrin alpha-M
Molecular weight formula_weight	22480.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GAMGSPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKGFAIEG

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

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4m76a1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.4 — Complement components

Domain ID domain_id	d4m76a2
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

Domain ID domain_id	d4m76b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.1 — Integrin A (or I) domain

CATH v4.4 (2 domains)

Domain ID domain_id	4m76A00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4m76B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

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Unit-cell length a length_a	144.460 Å
Unit-cell length b length_b	65.120 Å
Unit-cell length c length_c	62.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.804 Å
Low-resolution limit resolution_low	45.107 Å
R factor r_factor	0.1979
R_work r_work	0.1940
R_free r_free	0.2419

Integrin I domain of complement receptor 3 in complex with C3d

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

Complement C3

State in the Current Structure

Other States of the Same Protein in the Database

Integrin alpha-M

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

4m76__assembly_1__model_1

4m76__assembly_1__model_1 | I(q)

4m76__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Integrin I domain of complement receptor 3 in complex with C3d

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

Complement C3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Integrin alpha-M

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

4m76__assembly_1__model_1

4m76__assembly_1__model_1 | I(q)

4m76__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)