7ZLH: C-mannosyltransferase CeDPY19, in apo state

Cryo-EM structure of C-mannosyltransferase CeDPY19, in apo state, bound to CMT2-Fab and anti-Fab nanobody. Determined by electron microscopy at 2.75 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 2.75 Å
Organisms: synthetic construct, Caenorhabditis elegans
Chains: 4
Atoms: 9,481
Mol. weight: 142.52 kDa
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

7ZLH contains 47 α-helices and 60 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: 37 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	24-54	31
α-helix	56-58	3
α-helix	61-66	6
α-helix	71-84	14
α-helix	88-96	9
β-strand	98	1	14
β-strand	107	1	14
α-helix	116-135	20
β-strand	140-145	6	15
β-strand	153-158	6	15
α-helix	162-174	13
α-helix	176-189	14
α-helix	192-204	13
α-helix	206-209	4
α-helix	219-239	21
α-helix	245-260	16
α-helix	265-280	16
α-helix	287-307	21
α-helix	319-331	13
α-helix	334-336	3
β-strand	341	1	16
α-helix	342-365	24
α-helix	376-384	9
α-helix	390-396	7
α-helix	403-405	3
α-helix	406-414	9
α-helix	417-433	17
β-strand	440	1	16
α-helix	450-468	19
α-helix	473-484	12
α-helix	485-488	4
α-helix	500-516	17
α-helix	519-526	8
α-helix	535-547	13
β-strand	554-556	3	17
α-helix	558-566	9
β-strand	572	1	17
α-helix	584-590	7
α-helix	591-594	4
α-helix	599-609	11
β-strand	613-617	5	17
α-helix	618-620	3
α-helix	632-635	4
α-helix	641-643	3
α-helix	647-648	2
α-helix	650-656	7
β-strand	668-674	7	17
β-strand	678-683	6	17

Chain H: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13-15	3	2
β-strand	20-28	9	1
α-helix	31	1
β-strand	36-42	7	2
β-strand	48-55	8	2
β-strand	60-63	4	2
β-strand	72-76	5	1
β-strand	81-87	7	1
β-strand	95-102	8	2
α-helix	105-107	3
α-helix	112-114	3
β-strand	122-126	5	2
α-helix	133-134	2
β-strand	135-139	5	3
β-strand	151-160	10	3
β-strand	166-169	4	4
α-helix	170-172	3
β-strand	178-180	3	3
α-helix	181-183	3
β-strand	191-199	9	3
α-helix	204-206	3
β-strand	209-214	6	4
β-strand	215	1	5
β-strand	220	1	5
β-strand	223-226	4	4

Chain K: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	12	1	7
β-strand	17-25	9	6
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	59-60	2	8
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-84	7	6
β-strand	92-97	6	8
β-strand	98-99	2	9
β-strand	108-110	3	9
β-strand	115-117	3	8
β-strand	119	1	7

Chain L: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	10
β-strand	11-14	4	11
β-strand	20-26	7	10
β-strand	34-39	6	11
β-strand	46-50	5	11
β-strand	54-55	2	11
β-strand	63-68	6	10
β-strand	71-76	6	10
β-strand	86-91	6	11
β-strand	103-107	5	11
β-strand	115-119	5	12
β-strand	130-138	9	12
β-strand	147-150	4	13
β-strand	161-164	4	12
α-helix	165-168	4
β-strand	175-183	9	12
β-strand	192-197	6	13
α-helix	205	1
β-strand	206-211	6	13

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
C-mannosyltransferase dpy-19	A	protein	707	Caenorhabditis elegans	P34413 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7ZLH_1 CMT2-Fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSSSVYWSWWGYSAFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (K), FASTA

>7ZLH_2 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Sequence of entity 3 (L), FASTA

>7ZLH_3 CMT2-Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQGASEPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (A), FASTA

>7ZLH_4 C-mannosyltransferase dpy-19 (chains A)
MAKKPKNSPEKSKYSSDTSSSLYSQTWLASVVIIGLLVGYINYQHVYTLFENDKHFSHLA
DFEREMAYRTEMGLYYSYYKTIINAPSFLEGVQEITHDTVTEHGHEINTLNRFNLYPEVI
LAFLYRPFRAFAKSANWQIELCWQVNRGELRPVESCEGIGNPHYFYITGVFIVAGTVASS
IFYLGVLVSDSIFGGFLSVLCFAFNHGEATRVQWTPPLRESFAFPFIIGHIAILTFVIKY
KKSGHSMILLLTSMAVPALLFWQFTQFAFFTQICSIFLAFSLDLIPFSTAKTVIHSHIIS
FLIGFLLLFGNEMMITALYFPSILALGMIIYISPLLSNLKFRPAYVLFLAIIFASITLGL
KIGLSKGLGIEDDAHIFDILRSKFTSFANFHTRLYTCSAEFDFIQYSTIEKLCGTLLIPL
ALISLVTFVFNFVKNTNLLWRNSEEIGENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHL
CIVAALFANSKLLGGDRISKTIRVSALVGVIAILFYRGIPNIRQQLNVKGEYSNPDQEML
FDWIQHNTKQDAVFAGTMPVMANVKLTTLRPIVNHPHYEHVGIRERTLKVYSMFSKKPIA
EVHKIMKEMGVNYFVFQLMNCSNDERRPECVYRGMWDEEDPKNSGRTALCDLWILAANSK
DNSRIAPFKIVYNANRNYIVLKILEDYKDHDGDYKDHDIDYKDDDDK

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 P34413 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZLG 2.72 Å, Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with acceptor peptide and…
7ZLI 2.99 Å, Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and…
7ZLJ 3.63 Å, Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with…

Browse structure collections

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