7ZLG: C-mannosyltransferase CeDPY19

Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with acceptor peptide and bound to CMT2-Fab and anti-Fab nanobody. Determined by electron microscopy at 2.72 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 2.72 Å
Organisms: synthetic construct, Caenorhabditis elegans
Chains: 5
Atoms: 9,618
Mol. weight: 143.34 kDa
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

7ZLG contains 51 α-helices and 67 β-strands across 4 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: 39 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	26-54	29
α-helix	56-58	3
α-helix	61-67	7
α-helix	72-84	13
α-helix	88-96	9
β-strand	98	1	16
β-strand	107	1	16
α-helix	109-112	4
α-helix	116-134	19
β-strand	140-145	6	17
α-helix	151-152	2
β-strand	153-158	6	17
α-helix	162-187	26
α-helix	192-204	13
α-helix	206-209	4
α-helix	219-240	22
α-helix	245-260	16
α-helix	265-280	16
α-helix	287-307	21
α-helix	312-314	3
α-helix	319-331	13
α-helix	334-336	3
β-strand	341	1	18
α-helix	342-365	24
α-helix	375-384	10
α-helix	390-395	6
α-helix	403-405	3
α-helix	406-414	9
α-helix	418-435	18
β-strand	440	1	18
α-helix	450-468	19
α-helix	473-484	12
α-helix	485-488	4
α-helix	501-516	16
α-helix	519-526	8
α-helix	535-547	13
β-strand	554-556	3	19
α-helix	558-566	9
β-strand	572	1	19
α-helix	584-590	7
α-helix	591-594	4
α-helix	599-609	11
β-strand	613-617	5	19
α-helix	618-621	4
α-helix	632-639	8
α-helix	641-643	3
α-helix	647-648	2
α-helix	649-659	11
β-strand	668-674	7	19
β-strand	678-683	6	19

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14-15	2	2
β-strand	20-28	9	1
α-helix	31	1
β-strand	36-42	7	3
β-strand	48-55	8	3
β-strand	60-63	4	3
α-helix	65-67	3
β-strand	72-76	5	1
β-strand	81-87	7	1
β-strand	95-102	8	3
α-helix	105-107	3
α-helix	112-114	3
β-strand	119	1	1
β-strand	122-124	3	3
β-strand	125-126	2	2
β-strand	132	1	4
β-strand	135-139	5	5
β-strand	153-160	8	5
β-strand	161	1	4
β-strand	166-169	4	6
α-helix	170-172	3
β-strand	178-180	3	5
α-helix	181-183	3
β-strand	184-185	2	5
β-strand	191-197	7	5
α-helix	203-206	4
β-strand	210-214	5	6
β-strand	215	1	7
β-strand	220	1	7
β-strand	223-225	3	6

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	12	1	9
β-strand	18-25	8	8
β-strand	33-39	7	10
β-strand	46-51	6	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
β-strand	92-99	8	10
β-strand	108-110	3	10
β-strand	115-117	3	10
β-strand	119	1	9

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	11
β-strand	11-14	4	12
β-strand	20-26	7	11
β-strand	34-39	6	12
β-strand	46-50	5	12
β-strand	54-55	2	12
α-helix	56	1
β-strand	57	1	13
β-strand	59	1	13
β-strand	63-68	6	11
β-strand	71-76	6	11
β-strand	86-91	6	12
β-strand	99	1	12
β-strand	103-107	5	12
α-helix	113-114	2
β-strand	115-119	5	14
α-helix	123-126	4
β-strand	131-140	10	14
β-strand	145-150	6	15
β-strand	161-164	4	14
β-strand	174-182	9	14
α-helix	184-187	4
β-strand	192-199	8	15
β-strand	206-211	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CMT2-Fab heavy chain	H	protein	236	synthetic construct
Anti-Fab nanobody	K	protein	123	synthetic construct
CMT2-Fab light chain	L	protein	215	synthetic construct	Q7Z3Y4 (AlphaFold model)
C-mannosyltransferase dpy-19	A	protein	707	Caenorhabditis elegans	P34413 (AlphaFold model)
Synthetic octapeptide WEHI 1886493	P	protein	7	synthetic construct

Sequence of entity 1 (H), FASTA

>7ZLG_1 CMT2-Fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSSSVYWSWWGYSAFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (K), FASTA

>7ZLG_2 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Sequence of entity 3 (L), FASTA

>7ZLG_3 CMT2-Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQGASEPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (A), FASTA

>7ZLG_4 C-mannosyltransferase dpy-19 (chains A)
MAKKPKNSPEKSKYSSDTSSSLYSQTWLASVVIIGLLVGYINYQHVYTLFENDKHFSHLA
DFEREMAYRTEMGLYYSYYKTIINAPSFLEGVQEITHDTVTEHGHEINTLNRFNLYPEVI
LAFLYRPFRAFAKSANWQIELCWQVNRGELRPVESCEGIGNPHYFYITGVFIVAGTVASS
IFYLGVLVSDSIFGGFLSVLCFAFNHGEATRVQWTPPLRESFAFPFIIGHIAILTFVIKY
KKSGHSMILLLTSMAVPALLFWQFTQFAFFTQICSIFLAFSLDLIPFSTAKTVIHSHIIS
FLIGFLLLFGNEMMITALYFPSILALGMIIYISPLLSNLKFRPAYVLFLAIIFASITLGL
KIGLSKGLGIEDDAHIFDILRSKFTSFANFHTRLYTCSAEFDFIQYSTIEKLCGTLLIPL
ALISLVTFVFNFVKNTNLLWRNSEEIGENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHL
CIVAALFANSKLLGGDRISKTIRVSALVGVIAILFYRGIPNIRQQLNVKGEYSNPDQEML
FDWIQHNTKQDAVFAGTMPVMANVKLTTLRPIVNHPHYEHVGIRERTLKVYSMFSKKPIA
EVHKIMKEMGVNYFVFQLMNCSNDERRPECVYRGMWDEEDPKNSGRTALCDLWILAANSK
DNSRIAPFKIVYNANRNYIVLKILEDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 5 (P), FASTA

>7ZLG_5 Synthetic octapeptide WEHI 1886493 (chains P)
GSWAKWS

Primary citation

Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Bloch, J.S., John, A., Mao, R. et al. Nat Chem Biol (2023) 19:575-584. DOI 10.1038/s41589-022-01219-9 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MY5 1.73 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
4PUB 1.75 Å, Crystal structure of Fab DX-2930
1L7I 1.8 Å, Crystal Structure of the anti-ErbB2 Fab2C4
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
4OGY 2.1 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom…
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
9MY8 2.3 Å, D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
4OGX 2.4 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom…
8CWJ 2.45 Å, Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain…

Browse structure collections

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