1m3d

Structure of Type IV Collagen NC1 Domains

Method: X-RAY DIFFRACTION

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

Type IV Collagen Noncollagenous Domain- Alpha1

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	Type IV Collagen Noncollagenous Domain- Alpha2 × 2 （Q7SIB3） BROMIDE ION × 18 GLYCEROL × 4 LUTETIUM (III) ION × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Type IV Collagen Noncollagenous Domain- Alpha2 × 2 （Q7SIB3） BROMIDE ION × 18 GLYCEROL × 4 LUTETIUM (III) ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SIB2_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 1–229 Author chain B； PDBConstruct 1–229； UniProt 1–229 Author chain D； PDBConstruct 1–229； UniProt 1–229 Author chain E； PDBConstruct 1–229； UniProt 1–229 Author chain G； PDBConstruct 1–229； UniProt 1–229 Author chain H； PDBConstruct 1–229； UniProt 1–229 Author chain J； PDBConstruct 1–229； UniProt 1–229 Author chain K； PDBConstruct 1–229； UniProt 1–229

Type IV Collagen Noncollagenous Domain- Alpha2

OrganismNot specified

UniProt Q7SIB3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Type IV Collagen Noncollagenous Domain- Alpha1 × 4 （Q7SIB2） BROMIDE ION × 18 GLYCEROL × 4 LUTETIUM (III) ION × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Type IV Collagen Noncollagenous Domain- Alpha1 × 4 （Q7SIB2） BROMIDE ION × 18 GLYCEROL × 4 LUTETIUM (III) ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SIB3_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–227； UniProt 1–227 Author chain F； PDBConstruct 1–227； UniProt 1–227 Author chain I； PDBConstruct 1–227； UniProt 1–227 Author chain L； PDBConstruct 1–227； UniProt 1–227

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	1m3d
Deposition date deposition_date	2002-06-27
Structure title title	Structure of Type IV Collagen NC1 Domains
Keywords keywords	Basement membrane, Type IV collagen, NC1 domain, Network assembly, 3D domain swapping, Br-MAD, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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.

1m3d__assembly_1__model_1

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

Download this curve (.dat)

1m3d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m3d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.52 Å
Rg (electron density)	29.74 Å
Total Rg	30.59 Å
Atom count	10423
Residues	1341
Excluded volume	184350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m3d__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m3d__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Type IV Collagen Noncollagenous Domain- Alpha1
Molecular weight formula_weight	25399.9 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K
Atom count atom_count	22023

SVDHGFLVTRHSQTTDDPQCPPGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPQCPTGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

Entity 2 Entity 2 polymer

Description description	Type IV Collagen Noncollagenous Domain- Alpha2
Molecular weight formula_weight	25083.5 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

ISIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLPMMPVAEEDIRPYISRCSVCEAPAVAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGARGTCHYYANKYSFWLTTIPEQSFQGTPSADTLKAGLIRTHISRCQVCMKNL

Entity 3 Entity 3 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	LUTETIUM (III) ION
Molecular weight formula_weight	175.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1138

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1m3da1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3da2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3db1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3db2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3de1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3de2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3df1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3df2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3di1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3di2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dj1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dj2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dk2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dl1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

Domain ID domain_id	d1m3dl2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.6 — Noncollagenous (NC1) domain of collagen IV

CATH v4.4 (12 domains)

Domain ID domain_id	1m3dA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dE00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dF00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dG00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dH00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dI00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dJ00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dK00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

Domain ID domain_id	1m3dL00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	240 — Noncollagenous (NC1) domain of collagen IV
Homologous superfamily homologous superfamily	10 — Collagen IV, non-collagenous

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Unit-cell length a length_a	80.069 Å
Unit-cell length b length_b	137.963 Å
Unit-cell length c length_c	127.131 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1710
R_work r_work	0.1690
R_free r_free	0.1970

Structure of Type IV Collagen NC1 Domains

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

Type IV Collagen Noncollagenous Domain- Alpha1

State in the Current Structure

Other States of the Same Protein in the Database

Type IV Collagen Noncollagenous Domain- Alpha2

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

1m3d__assembly_1__model_1

1m3d__assembly_1__model_1 | I(q)

1m3d__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (24 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of Type IV Collagen NC1 Domains

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

Type IV Collagen Noncollagenous Domain- Alpha1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Type IV Collagen Noncollagenous Domain- Alpha2

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

1m3d__assembly_1__model_1

1m3d__assembly_1__model_1 | I(q)

1m3d__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (24 domains)

CATH v4.4 (12 domains)

7. Citations (1)