7STZ: Cadherin-1

Crystal Structure of Human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab mAb-1_19A11. Determined by X-ray diffraction at 2.95 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 14,687
Mol. weight: 239.28 kDa
Ligands: NAG, MAN, BMA, CA
Released: 26 Jan 2022

Explore 7STZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7STZ contains 51 α-helices and 179 β-strands across 6 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: 9 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
α-helix	4-6	3
β-strand	7-10	4	2
β-strand	19-23	5	3
β-strand	25-26	2	4
α-helix	27-30	4
β-strand	35-39	5	2
β-strand	41	1	5
β-strand	45	1	5
β-strand	51-53	3	3
β-strand	59-62	4	3
β-strand	73-81	9	2
β-strand	87	1	2
α-helix	90-91	2
β-strand	92-99	8	2
β-strand	107-108	2	6
β-strand	112-118	7	7
α-helix	121-122	2
β-strand	126-129	4	8
β-strand	132-133	2	6
β-strand	147-154	8	7
β-strand	163-165	3	8
β-strand	171-174	4	8
β-strand	186-194	9	7
α-helix	195-198	4
β-strand	202-212	11	7
α-helix	213	1
β-strand	220-221	2	9
β-strand	225-230	6	10
β-strand	240-242	3	11
β-strand	244-245	2	9
β-strand	257-261	5	10
β-strand	269-274	6	11
β-strand	279-284	6	11
β-strand	295-304	10	10
α-helix	307-308	2
β-strand	316-323	8	10
α-helix	324-325	2
α-helix	329-330	2
β-strand	331-332	2	12
β-strand	336-342	7	13
β-strand	350-353	4	14
β-strand	356-357	2	12
β-strand	368-373	6	13
β-strand	379-381	3	14
β-strand	387-390	4	14
β-strand	406-414	9	13
β-strand	422-432	11	13
β-strand	440-441	2	15
β-strand	445-453	9	16
β-strand	456-459	4	17
β-strand	460-461	2	15
β-strand	473-477	5	16
β-strand	484-488	5	17
β-strand	495-500	6	17
β-strand	507-516	10	16
β-strand	521-536	16	16

Chain D: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	4
α-helix	4-6	3
β-strand	7-10	4	30
β-strand	19-23	5	31
β-strand	25-26	2	1
α-helix	27-30	4
β-strand	35-39	5	30
β-strand	41	1	32
β-strand	45	1	32
β-strand	51-53	3	31
β-strand	59-62	4	31
β-strand	73-81	9	30
β-strand	87	1	30
α-helix	90-91	2
β-strand	92-99	8	30
β-strand	107-108	2	33
β-strand	112-118	7	34
α-helix	121-122	2
β-strand	126-129	4	35
β-strand	132-133	2	33
β-strand	147-154	8	34
β-strand	163-165	3	35
β-strand	171-174	4	35
β-strand	186-194	9	34
α-helix	196-198	3
β-strand	202-212	11	34
α-helix	213	1
β-strand	220-221	2	36
β-strand	225-230	6	37
β-strand	238-242	5	38
β-strand	244-245	2	36
β-strand	257-261	5	37
β-strand	269-274	6	38
β-strand	279-284	6	38
β-strand	295-304	10	37
β-strand	316-323	8	37
α-helix	324-325	2
α-helix	329-330	2
β-strand	331-332	2	39
β-strand	336-339	4	40
β-strand	350-353	4	41
α-helix	355	1
β-strand	356-357	2	39
α-helix	358	1
β-strand	368-373	6	40
β-strand	379-381	3	41
β-strand	387-390	4	41
β-strand	407-414	8	40
β-strand	425-429	5	40

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-12	2	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	46-51	6	20
β-strand	57-59	3	20
α-helix	64-66	3
β-strand	67-72	6	18
β-strand	77-82	6	18
α-helix	87-89	3
β-strand	91-98	8	20
α-helix	100-102	3
β-strand	108-109	2	20
β-strand	113-115	3	20
β-strand	116-117	2	19
α-helix	120-122	3
β-strand	123	1	21
β-strand	126-130	5	22
α-helix	141	1
β-strand	142-151	10	22
β-strand	152	1	21
β-strand	157-160	4	23
α-helix	161-163	3
β-strand	165	1	23
β-strand	169-171	3	22
α-helix	172-174	3
β-strand	175-177	3	22
β-strand	180-189	10	22
β-strand	200-205	6	23
β-strand	210-215	6	23

Chain I: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	42
β-strand	11-12	2	43
β-strand	18-25	8	42
β-strand	33-39	7	44
β-strand	46-51	6	44
β-strand	57-59	3	44
α-helix	64-66	3
β-strand	67-72	6	42
β-strand	77-82	6	42
α-helix	87-89	3
β-strand	91-98	8	44
α-helix	100-102	3
β-strand	108-109	2	44
β-strand	113-115	3	44
β-strand	116-117	2	43
α-helix	121-122	2
β-strand	123	1	45
β-strand	126-130	5	46
β-strand	141-151	11	46
β-strand	152	1	45
β-strand	157-160	4	47
α-helix	161-163	3
β-strand	165	1	47
β-strand	169-171	3	46
α-helix	172-174	3
β-strand	175-177	3	46
β-strand	180-190	11	46
β-strand	200-205	6	47
α-helix	206-208	3
β-strand	210-215	6	47

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-14	5	25
α-helix	17-18	2
β-strand	19-25	7	24
β-strand	30-31	2	26
β-strand	36-37	2	26
β-strand	39-44	6	25
β-strand	51-55	5	25
β-strand	59-60	2	25
α-helix	61	1
β-strand	68-73	6	24
β-strand	76-81	6	24
α-helix	86-88	3
β-strand	90-96	7	25
α-helix	102	1
β-strand	103-104	2	25
β-strand	108-113	6	25
β-strand	117	1	27
β-strand	120-124	5	28
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	28
β-strand	146	1	27
β-strand	150-156	7	29
β-strand	159-161	3	29
β-strand	165-169	5	28
α-helix	170-173	4
β-strand	179-188	10	28
α-helix	189-193	5
β-strand	197-204	8	29
β-strand	207-216	10	29

Chain M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	48
β-strand	10-14	5	49
α-helix	17-18	2
β-strand	19-25	7	48
β-strand	30-31	2	50
β-strand	36-37	2	50
β-strand	39-44	6	49
β-strand	51-55	5	49
β-strand	59-60	2	49
α-helix	61	1
β-strand	68-73	6	48
β-strand	76-81	6	48
α-helix	86-88	3
β-strand	90-96	7	49
α-helix	102	1
β-strand	103-104	2	49
β-strand	108-113	6	49
β-strand	117	1	51
β-strand	120-124	5	52
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	52
β-strand	146	1	51
β-strand	150-156	7	53
β-strand	159-161	3	53
β-strand	165-169	5	52
α-helix	170-173	4
β-strand	179-188	10	52
α-helix	189-193	5
β-strand	197-204	8	53
α-helix	210	1
β-strand	211-216	6	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cadherin-1	C, D	protein	590	Homo sapiens	P12830 (AlphaFold model)
mAb-1_19A11 Heavy Chain	H, I	protein	246	Mus musculus
mAb-1_19A11 Light Chain	L, M	protein	240	Mus musculus

Sequence of entity 1 (C, D), FASTA

>7STZ_1 Cadherin-1 (chains C, D)
MPLLLLLPLLWAGALADWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGAD
TPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDN
KPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFT
INRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTDTNDNPPIFNPT
TYKGQVPENEANVVITTLKVTDADAPNTPAWEAVYTILNDDGGQFVVTTNPVNNDGILKT
AKGLDFEAKQQYILHVAVTNVVPFEVSLTTSTATVTVDVLDVNEAPIFVPPEKRVEVSED
FGVGQEITSYTAQEPDTFMEQKITYRIWRDTANWLEINPDTGAISTRAELDREDFEHVKN
STYTALIIATDNGSPVATGTGTLLLILSDVNDNAPIPEPRTIFFCERNPKPQVINIIDAD
LPPNTSPFTAELTHGASANWTIQYNDPTQESIILKPKMALEVGDYKINLKLMDNQNKDQV
TTLEVSVCDCEGAAGVCRKASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (H, I), FASTA

>7STZ_2 mAb-1_19A11 Heavy Chain (chains H, I)
MAVLGLLLCLVTFPSCVLSQVQLKESGPGLVAPSQSLSITCTVSGFSLSRYGVHWVRQPP
GKGLEWLGMMWGGGNTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCASSNYV
LGYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC
HHHHHH

Sequence of entity 3 (L, M), FASTA

>7STZ_3 mAb-1_19A11 Light Chain (chains L, M)
MESQTQVLMFLLLWVSGACADIVMTQSPSSLAMSVGQKVTMNCKSSQSLLNSSNQKNYLA
WYQQKPGQSPKLLIYFTSTRGSGVPDRFIGSGSGTDFTLTISSVEAEDLADYFCQQHYRT
PHTFGGGTKVEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSE
RQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	3
BMA	beta-D-mannopyranose	C6 H12 O6	12
CA	Calcium ion	Ca	24

Water and common crystallization additives (EDO, PG4) 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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