9MQR: A8 Fab

A8 Fab in complex with CD97. Determined by electron microscopy at 3.16 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,729
Mol. weight: 108.53 kDa
Released: 24 Sept 2025

Explore 9MQR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MQR contains 11 α-helices and 44 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	266-267	2
α-helix	275-287	13
α-helix	294-310	17
α-helix	314-317	4
α-helix	320-342	23
β-strand	348-353	6	1
β-strand	359-364	6	1
β-strand	365	1	2
β-strand	371-375	5	3
β-strand	380-384	5	3
β-strand	397	1	2
β-strand	399-404	6	1
α-helix	408-411	4
β-strand	416-417	2	1
β-strand	438-441	4	1
β-strand	445-450	6	1
β-strand	462-467	6	3
β-strand	493-499	7	1
β-strand	507-509	3	1
β-strand	513-518	6	3
β-strand	522-527	6	3
β-strand	532-539	8	1

Chain D: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	4
β-strand	14-15	2	5
β-strand	21-28	8	4
α-helix	32-34	3
β-strand	36	1	6
β-strand	39-42	4	7
β-strand	48-55	8	7
β-strand	59-63	5	7
β-strand	72	1	4
β-strand	75-76	2	4
β-strand	81-86	6	4
α-helix	91-93	3
β-strand	95-99	5	7
β-strand	101-103	3	6
α-helix	105-107	3
β-strand	119-122	4	6
β-strand	127-129	3	7
β-strand	130-131	2	5

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	7	1	3
β-strand	10-13	4	9
β-strand	19-22	4	3
β-strand	25	1	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	3
β-strand	71-75	5	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adhesion G protein-coupled receptor E5	A	protein	542	Homo sapiens	P48960 (AlphaFold model)
Heavy chain of A8 Fab	D	protein	240	Homo sapiens
Light chain of A8 Fab	E	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>9MQR_1 Adhesion G protein-coupled receptor E5 (chains A)
QDSRGCARWCPQNSSCVNATACRCNPGFSSFSEIITTPTETCDDINECATPSKVSCGKFS
DCWNTEGSYDCVCSPGYEPVSGAKTFKNESENTCQDVDECQQNPRLCKSYGTCVNTLGSY
TCQCLPGFKFIPEDPKVCTDVNECTSGQNPCHSSTHCLNNVGSYQCRCRPGWQPIPGSPN
GPNNTVCEDVDECSSGQHQCDSSTVCFNTVGSYSCRCRPGWKPRHGIPNNQKDTVCEDMT
FSTWTPPPGVHSQTLSRFFDKVQDLGRDSKTSSAEVTIQNVIKLVDELMEAPGDVEALAP
PVRHLIATQLLSNLEDIMRILAKSLPKGPFTYISPSNTELTLMIQERGDKNVTMGQSSAR
MKLNWAVAAGAEDPGPAVAGILSIQNMTTLLANASLNLHSKKQAELEEIYESSIRGVQLR
RLSAVNSIFLSHNNTKELNSPILFAFSHLESSDGEAGRDPPAKDVMPGPRQELLCAFWKS
DSDRGGHWATEGCQVLGSKNGSTTCQCSHLASFAILMAHYDVEDWKLTLITRSSSSHHHH
HH

Sequence of entity 2 (D), FASTA

>9MQR_2 Heavy chain of A8 Fab (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFTISSYSIHWVRQAPGKGLEWVASISPYYGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSWYYYEQNPYWYQKEEQAL
DYWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (E), FASTA

>9MQR_3 Light chain of A8 Fab (chains E)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSVYSPVTFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Engineering antibody-drug conjugates targeting an adhesion GPCR, CD97. Hattori, T., Wang, M., Corrado, A.D. et al. Proc Natl Acad Sci U S A (2025) 122:e2516627122-e2516627122. DOI 10.1073/pnas.2516627122 · PubMed

Other PDB entries of the same protein (UniProt P48960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BOU 1.9 Å, EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with barium.
8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
7YDM 2.89 Å, Cryo-EM structure of CD97/Gq complex
7YDJ 3.03 Å, Cryo EM structure of CD97/miniG12 complex
7YDH 3.1 Å, Cryo EM structure of CD97/miniG13 complex
7YDP 3.1 Å, Cryo-EM structure of CD97/miniGs complex
7DO4 3.2 Å, Crystal structure of CD97-CD55 complex
8IKJ 3.2 Å, Cryo-EM structure of the inactive CD97

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