7ZLI: C-mannosyltransferase CeDPY19

Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody. Determined by electron microscopy at 2.99 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 2.99 Å
Organisms: synthetic construct, Caenorhabditis elegans
Chains: 4
Atoms: 9,582
Mol. weight: 143.13 kDa
Ligands: IZY
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

7ZLI contains 49 α-helices and 65 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	15
β-strand	107	1	15
α-helix	110-113	4
α-helix	116-135	20
β-strand	140-145	6	16
α-helix	151-152	2
β-strand	153-158	6	16
α-helix	162-174	13
α-helix	177-189	13
α-helix	192-204	13
α-helix	220-239	20
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	17
α-helix	342-362	21
α-helix	364-369	6
α-helix	375-378	4
α-helix	381-384	4
α-helix	389-396	8
α-helix	403-405	3
α-helix	406-414	9
α-helix	418-434	17
β-strand	440	1	17
α-helix	450-468	19
α-helix	473-484	12
α-helix	485-488	4
α-helix	500-526	27
α-helix	535-547	13
β-strand	554-556	3	18
α-helix	558-566	9
β-strand	572	1	18
α-helix	586-591	6
α-helix	592-594	3
α-helix	599-609	11
β-strand	613-617	5	18
α-helix	618-621	4
α-helix	632-638	7
α-helix	641-643	3
α-helix	647-648	2
α-helix	649-659	11
β-strand	668-674	7	18
β-strand	678-683	6	18

Chain H: 5 helices, 21 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	71-76	6	1
β-strand	81-87	7	1
β-strand	95-102	8	2
α-helix	112-114	3
β-strand	117-118	2	2
β-strand	122-126	5	2
β-strand	132	1	3
β-strand	135-139	5	4
α-helix	140-142	3
β-strand	151-160	10	4
β-strand	161	1	3
β-strand	166-169	4	5
α-helix	170-172	3
β-strand	178-180	3	4
β-strand	184-185	2	4
β-strand	191-199	9	4
α-helix	203-206	4
β-strand	209-215	7	5
β-strand	220-226	7	5

Chain K: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	12	1	7
β-strand	18-25	8	6
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	58-60	3	8
β-strand	61	1	9
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
β-strand	92-97	6	8
β-strand	98-99	2	10
β-strand	108-110	3	10
β-strand	115-117	3	8
β-strand	119	1	7

Chain L: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	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	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
β-strand	111	1	9
β-strand	115-119	5	13
α-helix	123-126	4
β-strand	130-140	11	13
β-strand	147-150	4	14
β-strand	160-164	5	13
α-helix	165-168	4
β-strand	174-183	10	13
α-helix	184-187	4
β-strand	192-199	8	14
β-strand	202-211	10	14

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)

Sequence of entity 1 (H), FASTA

>7ZLI_1 CMT2-Fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSSSVYWSWWGYSAFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (K), FASTA

>7ZLI_2 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Sequence of entity 3 (L), FASTA

>7ZLI_3 CMT2-Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQGASEPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (A), FASTA

>7ZLI_4 C-mannosyltransferase dpy-19 (chains A)
MAKKPKNSPEKSKYSSDTSSSLYSQTWLASVVIIGLLVGYINYQHVYTLFENDKHFSHLA
DFEREMAYRTEMGLYYSYYKTIINAPSFLEGVQEITHDTVTEHGHEINTLNRFNLYPEVI
LAFLYRPFRAFAKSANWQIELCWQVNRGELRPVESCEGIGNPHYFYITGVFIVAGTVASS
IFYLGVLVSDSIFGGFLSVLCFAFNHGEATRVQWTPPLRESFAFPFIIGHIAILTFVIKY
KKSGHSMILLLTSMAVPALLFWQFTQFAFFTQICSIFLAFSLDLIPFSTAKTVIHSHIIS
FLIGFLLLFGNEMMITALYFPSILALGMIIYISPLLSNLKFRPAYVLFLAIIFASITLGL
KIGLSKGLGIEDDAHIFDILRSKFTSFANFHTRLYTCSAEFDFIQYSTIEKLCGTLLIPL
ALISLVTFVFNFVKNTNLLWRNSEEIGENGEILYNVVQLCCSTVMAFLIMRLKLFMTPHL
CIVAALFANSKLLGGDRISKTIRVSALVGVIAILFYRGIPNIRQQLNVKGEYSNPDQEML
FDWIQHNTKQDAVFAGTMPVMANVKLTTLRPIVNHPHYEHVGIRERTLKVYSMFSKKPIA
EVHKIMKEMGVNYFVFQLMNCSNDERRPECVYRGMWDEEDPKNSGRTALCDLWILAANSK
DNSRIAPFKIVYNANRNYIVLKILEDYKDHDGDYKDHDIDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
IZY	Dolichol monophosphate beta-D-Mannose	C31 H55 O9 P	1

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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