1li1

The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link

Method: X-RAY DIFFRACTION

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

Collagen alpha 1(IV)

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	Collagen alpha 2(IV) × 2 （P08572） ACETATE ION × 9 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 E； PDBConstruct 1–229； UniProt 1441–1669

Collagen alpha 2(IV)

OrganismNot specified

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) × 4 （P02462） ACETATE ION × 9 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 F； 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	1li1
Deposition date deposition_date	2002-04-17
Structure title title	The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link
Keywords keywords	basement membrane, collagen IV, NC1 domain, covalent cross-link, protein-protein interaction, 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.

1li1__assembly_1__model_1

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

Download this curve (.dat)

1li1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1li1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.81 Å
Rg (electron density)	29.90 Å
Total Rg	30.90 Å
Atom count	10550
Residues	1359
Excluded volume	186310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1li1__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)
Molecular weight formula_weight	25356.9 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	11664

SVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT

Entity 2 Entity 2 polymer

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

Polymer Polymer

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

SVSIGYLLVKHSQTDQEPMCPVGMNKLWSGYSLLYFEGQEKAHNQDLGLAGSCLARFSTMPFLYCNPGDVCYYASRNDKSYWLSTTAPLPMMPVAEDEIKPYISRCSVCEAPAIAIAVHSQDVSIPHCPAGWRSLWIGYSFLMHTAAGDEGGGQSLVSPGSCLEDFRATPFIECNGGRGTCHYYANKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMKNL

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1114

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1li1a1
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	d1li1a2
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	d1li1b1
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	d1li1b2
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	d1li1c1
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	d1li1c2
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	d1li1d1
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	d1li1d2
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	d1li1e1
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	d1li1e2
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	d1li1f1
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	d1li1f2
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	1li1A00
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	1li1B00
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	1li1C00
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	1li1D00
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	1li1E00
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	1li1F00
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	234.589 Å
Unit-cell length b length_b	234.589 Å
Unit-cell length c length_c	99.492 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	36

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2020

The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link

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

Collagen alpha 1(IV)

State in the Current Structure

Other States of the Same Protein in the Database

Collagen alpha 2(IV)

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

1li1__assembly_1__model_1

1li1__assembly_1__model_1 | I(q)

1li1__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

Entity 2 Entity 2 polymer

Polymer Polymer

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)

The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link

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

Collagen alpha 1(IV)

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)

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

1li1__assembly_1__model_1

1li1__assembly_1__model_1 | I(q)

1li1__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

Entity 2 Entity 2 polymer

Polymer Polymer

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)