5nax

Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1

Method: X-RAY DIFFRACTION

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

Collagen alpha-1(IV) chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Collagen alpha-2(IV) chain × 2 （P08572） CHLORIDE ION × 11 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO4A1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 1441–1669 Author chain B； PDBConstruct 1–229； UniProt 1441–1669 Author chain D； PDBConstruct 1–229； UniProt 1441–1669 Author chain F； PDBConstruct 1–229； UniProt 1441–1669

Collagen alpha-2(IV) chain

Homo sapiens

UniProt P08572

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Collagen alpha-1(IV) chain × 4 （P02462） CHLORIDE ION × 11 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CO4A2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–228； UniProt 1485–1712 Author chain E； PDBConstruct 1–228； UniProt 1485–1712

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	5nax
Deposition date deposition_date	2017-02-28
Structure title title	Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1
Keywords keywords	Non-collagenous domain of collagen type IV, A principal structural component of basement membranes, 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.

5nax__assembly_1__model_1

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

Download this curve (.dat)

5nax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nax__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.68 Å
Rg (electron density)	29.78 Å
Total Rg	30.77 Å
Atom count	10402
Residues	1348
Excluded volume	183840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nax__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Collagen alpha-1(IV) chain
Molecular weight formula_weight	25356.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,F
Atom count atom_count	10565

SVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Collagen alpha-2(IV) chain
Molecular weight formula_weight	25114.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SVSIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLPMMPVAEDEIKPYISRCSVCEAPAIAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGTCHYYANKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMKNL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5naxa1
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	d5naxa2
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	d5naxb1
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	d5naxb2
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	d5naxc1
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	d5naxc2
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	d5naxd1
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	d5naxd2
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	d5naxe1
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	d5naxe2
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	d5naxf1
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	d5naxf2
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	5naxA00
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	5naxB00
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	5naxC00
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	5naxD00
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	5naxE00
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	5naxF00
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	126.148 Å
Unit-cell length b length_b	126.148 Å
Unit-cell length c length_c	216.211 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.820 Å
Low-resolution limit resolution_low	48.450 Å
R factor r_factor	0.1431
R_work r_work	0.1409
R_free r_free	0.1848

Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1

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

Collagen alpha-1(IV) chain

State in the Current Structure

Other States of the Same Protein in the Database

Collagen alpha-2(IV) 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

5nax__assembly_1__model_1

5nax__assembly_1__model_1 | I(q)

5nax__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1

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

Collagen alpha-1(IV) 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

Collagen alpha-2(IV) 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

5nax__assembly_1__model_1

5nax__assembly_1__model_1 | I(q)

5nax__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) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)