6VEL: 66E8 Fab Heavy Chain

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab. Determined by X-ray diffraction at 2.65 Å resolution. Released 29 Jan 2020.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 3
Atoms: 4,889
Mol. weight: 89.54 kDa
Ligands: CA
Released: 29 Jan 2020

Explore 6VEL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VEL contains 21 α-helices and 59 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 C: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	105-107	3
β-strand	108-111	4	9
β-strand	120-124	5	10
α-helix	128-130	3
β-strand	138-141	4	9
β-strand	152-155	4	10
β-strand	160-163	4	10
β-strand	174-180	7	9
β-strand	193-200	8	9
α-helix	201	1
β-strand	208-209	2	11
β-strand	213-219	7	12
α-helix	222-223	2
β-strand	227-230	4	13
β-strand	233-234	2	11
β-strand	248-255	8	12
β-strand	264-266	3	13
β-strand	272-275	4	13
β-strand	287-295	9	12
α-helix	297-299	3
β-strand	303-313	11	12

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	1
β-strand	29-31	3	2
β-strand	37-44	8	1
α-helix	48-50	3
β-strand	53-58	6	2
β-strand	64-70	7	2
β-strand	77-79	3	2
α-helix	81-83	3
β-strand	84	1	1
β-strand	87-92	6	1
α-helix	93-95	3
β-strand	97-102	6	1
α-helix	107-109	3
β-strand	111-117	7	2
β-strand	124-125	2	2
β-strand	126	1	1
β-strand	129-133	5	2
α-helix	136-138	3
α-helix	140-141	2
β-strand	142-146	5	3
β-strand	158-167	10	3
β-strand	173-176	4	4
α-helix	177-179	3
β-strand	181	1	4
β-strand	185-187	3	3
α-helix	188-190	3
β-strand	191-193	3	3
β-strand	196-205	10	3
α-helix	211-214	4
β-strand	215-221	7	4
α-helix	222-224	3
β-strand	226-232	7	4

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	5
β-strand	29-32	4	2
β-strand	38-44	7	5
β-strand	52-57	6	2
β-strand	64-68	5	2
β-strand	72-73	2	2
α-helix	74	1
β-strand	81-85	5	5
β-strand	89-94	6	5
α-helix	99-101	3
β-strand	104-109	6	2
α-helix	115	1
β-strand	116-117	2	2
β-strand	121-125	5	2
β-strand	130	1	6
α-helix	131-132	2
β-strand	133-137	5	7
α-helix	141-146	6
β-strand	148-158	11	7
β-strand	159	1	6
β-strand	164-169	6	8
β-strand	172-173	2	8
β-strand	178-182	5	7
β-strand	192-201	10	7
α-helix	202-205	4
β-strand	211-216	6	8
β-strand	224-228	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
66E8 Fab Heavy Chain	H	protein	243	Mus musculus
66E8 Fab Light Chain	L	protein	233	Mus musculus
Ubiquitin-like protein SMT3,Cadherin-1	C	protein	331	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens	P12830 (AlphaFold model), Q12306 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6VEL_1 66E8 Fab Heavy Chain (chains H)
MGWSCIILFLVATATGVHSEVQLQQSGPELVKPGASVKISCKASGYSFTGYFMNWVKQSH
GKSLEWIGRINPYNGDTFYKQRFKGKATLTVDKSSSTVHMDLLSLTSEDSAVYYCGRGNY
YFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGS
LSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCHHH
HHH

Sequence of entity 2 (L), FASTA

>6VEL_2 66E8 Fab Light Chain (chains L)
MGWSCIILFLVATATGVHSDVQITQSPSYLAASPGETITINCRTSKNISKYLAWYQEKPG
KTNKLLIYSGYTLQSGIPSRFSGSGSGTDFTLTISSLEPEDFAMYYCQQHNEYPYTFGGG
TKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLN
SWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C), FASTA

>6VEL_3 Ubiquitin-like protein SMT3,Cadherin-1 (chains C)
MASMHHHHHHGSSMASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTP
LRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGDWVIPP
ISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPL
DRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTS
VMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPT
YTLVVQAADLQGEGLSTTATAVITVTDTNDN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography. Maker, A., Bolejack, M., Schecterson, L. et al. PNAS Nexus (2022) 1:pgac163-pgac163. DOI 10.1093/pnasnexus/pgac163 · PubMed

Other PDB entries of the same protein (UniProt P12830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OMZ 1.6 Å, Crystal structure of InlA Y369A/hEC1 complex
2OMX 1.7 Å, Crystal structure of InlA S192N G194S+S/hEC1 complex
2OMY 1.7 Å, Crystal structure of InlA S192N/hEC1 complex
1O6S 1.8 Å, Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex
2OMU 1.8 Å, Crystal structure of InlA G194S+S Y369S/hEC1 complex
3FF7 1.8 Å, Structure of NK cell receptor KLRG1 bound to E-cadherin
2OMV 1.9 Å, Crystal structure of InlA S192N Y369S/hEC1 complex
8H62 1.91 Å, Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12
4ZT1 1.92 Å, Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation
2O72 2.0 Å, Crystal Structure Analysis of human E-cadherin (1-213)
2OMT 2.0 Å, Crystal structure of InlA G194S+S/hEC1 complex
3FF8 2.0 Å, Structure of NK cell receptor KLRG1 bound to E-cadherin

Browse structure collections

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