1GL4: Nidogen-1 G2/Perlecan IG3 Complex

Nidogen-1 G2/Perlecan IG3 Complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 28 Nov 2001.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: MUS MUSCULUS
Chains: 2
Atoms: 2,993
Mol. weight: 42.22 kDa
Ligands: ZN
Released: 28 Nov 2001

Explore 1GL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1GL4 contains 14 α-helices and 29 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	360-363	4
α-helix	364-366	3
β-strand	371-375	5	1
β-strand	380-384	5	1
α-helix	385	1
β-strand	388-390	3	2
β-strand	395-397	3	2
β-strand	401-414	14	3
β-strand	421-433	13	3
β-strand	438-444	7	3
α-helix	448-451	4
α-helix	452-454	3
α-helix	459-467	9
α-helix	469	1
β-strand	470-471	2	3
α-helix	478-482	5
β-strand	485-494	10	3
β-strand	501-508	8	3
β-strand	510	1	3
β-strand	516-517	2	3
β-strand	519-526	8	3
β-strand	534-536	3	3
β-strand	540-547	8	3
β-strand	550-562	13	3
α-helix	569-572	4
β-strand	573-584	12	3
α-helix	595-598	4
β-strand	600-613	14	3
β-strand	618-628	11	3

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1770-1774	5	4
α-helix	1775	1
β-strand	1779-1782	4	5
β-strand	1788-1791	4	6
β-strand	1792-1796	5	4
β-strand	1802-1807	6	5
α-helix	1808-1810	3
β-strand	1811	1	5
α-helix	1812-1814	3
β-strand	1817-1820	4	6
β-strand	1823-1826	4	6
α-helix	1831-1833	3
β-strand	1835-1842	8	5
β-strand	1847-1856	10	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nidogen-1	A	protein	285	MUS MUSCULUS	P10493 (AlphaFold model)
Basement membrane-specific heparan sulfate proteoglycan core protein	B	protein	98	MUS MUSCULUS	Q05793

Sequence of entity 1 (A), FASTA

>1GL4_1 NIDOGEN-1 (chains A)
APLAQQTCANNRHQCSVHAECRDYATGFCCRCVANYTGNGRQCVAEGSPQRVNGKVKGRI
FVGSSQVPVVFENTDLHSYVVMNHGRSYTAISTIPETVGYSLLPLAPIGGIIGWMFAVEQ
DGFKNGFSITGGEFTRQAEVTFLGHPGKLVLKQQFSGIDEHGHLTISTELEGRVPQIPYG
ASVHIEPYTELYHYSSSVITSSSTREYTVMEPDQDGAAPSHTHIYQWRQTITFQECAHDD
ARPALPSTQQLSVDSVFVLYNKEERILRYALSNSIGPVRDGSPDA

Sequence of entity 2 (B), FASTA

>1GL4_2 BASEMENT MEMBRANE-SPECIFIC HEPARAN SULFATE PROTEOGLYCAN CORE PROTEIN (chains B)
APLAAPSKPIMVTVEEQRSQSVRPGADVTFICTAKSKSPAYTLVWTRLHNGKLPSRAMDF
NGILTIRNVQPSDAGTYVCTGSNMFAMDQGTATLHVQV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EPE) are not listed.

Primary citation

Structural Basis for the High-Affinity Interaction of Nidogen-1 with Immunoglobulin-Like Domain 3 of Perlecan. Kvansakul, M., Hopf, M., Ries, A. et al. EMBO J (2001) 20:5342. DOI 10.1093/EMBOJ/20.19.5342 · PubMed

Other PDB entries of the same protein (UniProt P10493 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1H4U 2.2 Å, Domain G2 of mouse nidogen-1
1NPE 2.3 Å, Crystal structure of Nidogen/Laminin Complex

Browse structure collections

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