1t61

crystal structure of collagen IV NC1 domain from placenta basement membrane

Method: X-RAY DIFFRACTION

▼

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

Type IV Collagen

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 × 4 POTASSIUM ION × 6 CHLORIDE ION × 6 GLYCEROL × 7 CALCIUM ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO4A2_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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1t61
Deposition date deposition_date	2004-05-05
Structure title title	crystal structure of collagen IV NC1 domain from placenta basement membrane
Keywords keywords	basement membrane, type IV collagen, NC1 domain, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1t61__assembly_1__model_1

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

Download this curve (.dat)

1t61__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t61__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.64 Å
Rg (electron density)	29.70 Å
Total Rg	30.67 Å
Atom count	10415
Residues	1338
Excluded volume	184590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t61__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Type IV Collagen
Molecular weight formula_weight	25399.9 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	11088

SVDHGFLVTRHSQTTDDPQCPPGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPQCPTGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

Entity 2 Entity 2 polymer

Description description	Type IV Collagen
Molecular weight formula_weight	25083.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

ISIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLPMMPVAEEDIRPYISRCSVCEAPAVAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGARGTCHYYANKYSFWLTTIPEQSFQGTPSADTLKAGLIRTHISRCQVCMKNL

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

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	7

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	673

▼

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1t61a1
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	d1t61a2
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	d1t61b1
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	d1t61b2
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	d1t61c1
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	d1t61c2
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	d1t61d1
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	d1t61d2
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	d1t61e1
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	d1t61e2
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	d1t61f1
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	d1t61f2
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 (6 domains)

Domain ID domain_id	1t61A00
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	1t61B00
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	1t61C00
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	1t61D00
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	1t61E00
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	1t61F00
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

▶

Unit-cell length a length_a	73.650 Å
Unit-cell length b length_b	80.139 Å
Unit-cell length c length_c	235.420 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1770
R_work r_work	0.1740
R_free r_free	0.2000

crystal structure of collagen IV NC1 domain from placenta basement membrane

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

Type IV Collagen

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

1t61__assembly_1__model_1

1t61__assembly_1__model_1 | I(q)

1t61__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

crystal structure of collagen IV NC1 domain from placenta basement membrane

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

Type IV Collagen

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

1t61__assembly_1__model_1

1t61__assembly_1__model_1 | I(q)

1t61__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)