8DMK: Laminin subunit alpha-1

Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies. Determined by electron microscopy at 3.7 Å resolution. Released 1 Feb 2023.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 7,348
Mol. weight: 105.06 kDa
Ligands: CA, NAG
Released: 1 Feb 2023

Explore 8DMK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DMK contains 30 α-helices and 65 β-strands across 3 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: 14 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
α-helix	30-33	4
β-strand	34-35	2	2
β-strand	41-44	4	2
β-strand	50	1	3
β-strand	52	1	3
β-strand	54-57	4	4
α-helix	62-64	3
β-strand	73-76	4	4
β-strand	77	1	5
β-strand	86	1	5
α-helix	89-91	3
β-strand	100-101	2	6
α-helix	102-104	3
α-helix	109-112	4
β-strand	114-132	19	2
α-helix	137-139	3
β-strand	141-147	7	2
β-strand	153-159	7	2
α-helix	163-165	3
α-helix	166-170	5
α-helix	173	1
β-strand	174	1	2
α-helix	175-176	2
β-strand	189-190	2	2
β-strand	203-207	5	2
α-helix	220-225	6
β-strand	227-237	11	2
α-helix	243-246	4
α-helix	258-261	4
β-strand	267-268	2	6
β-strand	270	1	2
β-strand	273-277	5	2
β-strand	282	1	1
α-helix	287	1
β-strand	288-289	2	7
β-strand	294-295	2	7
β-strand	304	1	8
β-strand	310	1	8

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	36-39	4
β-strand	40-41	2	9
β-strand	50-52	3	10
β-strand	63	1	11
β-strand	78	1	11
α-helix	105-109	5
β-strand	112-113	2	9
β-strand	121-125	5	10
β-strand	131-132	2	12
β-strand	135-140	6	9
β-strand	147-152	6	10
β-strand	161-167	7	10
α-helix	170-173	4
β-strand	190-191	2	10
β-strand	204-206	3	9
α-helix	222-225	4
β-strand	229-230	2	12
β-strand	234-239	6	10
α-helix	255-257	3
β-strand	261-269	9	9
β-strand	271	1	12
α-helix	281-283	3
β-strand	305	1	13
β-strand	311	1	13
β-strand	325	1	14
β-strand	328	1	14
α-helix	331-334	4

Chain G: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	15
β-strand	56	1	16
β-strand	63-65	3	17
β-strand	74-75	2	18
α-helix	80-82	3
β-strand	91-92	2	18
α-helix	103-105	3
β-strand	118-119	2	16
α-helix	123-125	3
β-strand	128-143	16	17
β-strand	147-152	6	16
β-strand	159-163	5	17
β-strand	174-179	6	17
α-helix	182-185	4
β-strand	204-206	3	17
β-strand	218-223	6	16
α-helix	234-236	3
α-helix	238-244	7
β-strand	246-255	10	17
α-helix	261-263	3
α-helix	267-270	4
β-strand	276-283	8	16
β-strand	286	1	17
β-strand	291	1	15
β-strand	292-297	6	19
β-strand	303-307	5	19
β-strand	311-312	2	20
β-strand	318-319	2	20
α-helix	321-323	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Laminin subunit alpha-1	A	protein	305	Mus musculus	P19137
Laminin subunit beta-1	B	protein	307	Homo sapiens	P07942 (AlphaFold model)
Laminin subunit gamma-1	G	protein	305	Homo sapiens	P11047 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DMK_1 Laminin subunit alpha-1 (chains A)
GLFPAILNLATNAHISANATCGEKGPEMFCKLVEHVPGRPVRHAQCRVCDGNSTNPRERH
PISHAIDGTNNWWQSPSIQNGREYHWVTVTLDLRQVFQVAYIIIKAANAPRPGNWILERS
VDGVKFKPWQYYAVSDTECLTRYKITPRRGPPTYRADNEVICTSYYSKLVPLEHGEIHTS
LINGRPSADDPSPQLLEFTSARYIRLRLQRIRTLNADLMTLSHRDLRDLDPIVTRRYYYS
IKDISVGGMCICYGHASSCPWDEEAKQLQCQCEHNTCGESCDRCCPGYHQQPWRPGTISS
GNECE

Sequence of entity 2 (B), FASTA

>8DMK_2 Laminin subunit beta-1 (chains B)
GCAEGSCYPATGDLLIGRAQKLSVTSTCGLHKPEPYCIVSHLQEDKKCFICNSQDPYHET
LNPDSHLIENVVTTFAPNRLKIWWQSENGVENVTIQLDLEAEFHFTHLIMTFKTFRPAAM
LIERSSDFGKTWGVYRYFAYDCEASFPGISTGPMKKVDDIICDSRYSDIEPSTEGEVIFR
ALDPAFKIEDPYSPRIQNLLKITNLRIKFVKLHTLGDNLLDSRMEIREKYYYAVYDMVVR
GNCFCYGHASECAPVDGFNEEVEGMVHGHCMCRHNTKGLNCELCMDFYHDLPWRPAEGRN
SNACKKC

Sequence of entity 3 (G), FASTA

>8DMK_3 Laminin subunit gamma-1 (chains G)
MDECTDEGGRPQRCMPEFVNAAFNVTVVATNTCGTPPEEYCVQTGVTGVTKSCHLCDAGQ
PHLQHGAAFLTDYNNQADTTWWQSQTMLAGVQYPSSINLTLHLGKAFDITYVRLKFHTSR
PESFAIYKRTWEDGPWIPYQYYSGSCENTYSKANRGFIRTGGDEQQALCTDEFSDISPLT
GGNVAFSTLEGRPSAYNFDNSPVLQEWVTATDISVTLNRLNTFGDEVFNDPKVLKSYYYA
ISDFAVGGRCKCNGHASECMKNEFDKLVCNCKHNTYGVDCEKCLPFFNDRPWRRATAESA
SECLP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Cryo-EM reveals the molecular basis oflaminin polymerization and LN-lamininopathies. Kulczyk, A.W., McKee, K.K., Zhang, X. et al. Nat Commun (2023) 14:317-317. DOI 10.1038/s41467-023-36077-z · PubMed

Other PDB entries of the same protein (UniProt P19137), best resolution first:

2JD4 1.9 Å, Mouse laminin alpha1 chain, domains LG4-5
5MC9 2.13 Å, Crystal structure of the heterotrimeric integrin-binding region of laminin-111

Browse structure collections

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