7ZLJ: CMT2-Fab heavy chain

Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody. Determined by electron microscopy at 3.63 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 3.63 Å
Organisms: synthetic construct, Caenorhabditis elegans
Chains: 5
Atoms: 9,659
Mol. weight: 143.95 kDa
Ligands: IZU
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

7ZLJ contains 48 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: 37 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	70-84	15
α-helix	88-95	8
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	220-240	21
α-helix	245-260	16
α-helix	265-280	16
α-helix	287-307	21
α-helix	312-314	3
α-helix	320-332	13
α-helix	333-336	4
β-strand	341	1	17
α-helix	342-368	27
α-helix	375-384	10
α-helix	391-396	6
α-helix	403-405	3
α-helix	406-414	9
α-helix	417-434	18
β-strand	440	1	17
α-helix	450-468	19
α-helix	473-483	11
α-helix	484-488	5
α-helix	501-516	16
α-helix	519-527	9
α-helix	535-547	13
β-strand	554-556	3	18
α-helix	558-566	9
β-strand	572	1	18
α-helix	584-590	7
α-helix	591-594	4
α-helix	599-609	11
β-strand	613-617	5	18
α-helix	632-638	7
α-helix	647-648	2
α-helix	649-659	11
β-strand	668-674	7	18
β-strand	678-683	6	18

Chain H: 6 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	35-42	8	2
β-strand	48-55	8	2
β-strand	60-63	4	2
α-helix	65-67	3
β-strand	71-76	6	1
β-strand	81-87	7	1
β-strand	95-103	9	2
α-helix	112-114	3
β-strand	118	1	2
β-strand	122-126	5	2
β-strand	135-139	5	3
β-strand	153-158	6	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	184-185	2	3
β-strand	191-197	7	3
α-helix	203-206	4
β-strand	210-214	5	4
β-strand	215	1	5
β-strand	220	1	5
β-strand	223-225	3	4

Chain K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	17-25	9	6
β-strand	34-39	6	7
β-strand	46-51	6	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	65	1	6
β-strand	68-73	6	6
β-strand	78-84	7	6
β-strand	92-98	7	7
β-strand	99	1	8
β-strand	108	1	8
β-strand	115-117	3	7

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	9
β-strand	11-13	3	10
β-strand	20-26	7	9
β-strand	34-39	6	10
β-strand	46-50	5	10
β-strand	54-55	2	10
β-strand	57	1	11
β-strand	59	1	11
β-strand	63-68	6	9
β-strand	71-76	6	9
β-strand	86-91	6	10
α-helix	98-100	3
β-strand	103-106	4	10
β-strand	115-119	5	12
α-helix	123-126	4
β-strand	130-138	9	12
β-strand	150-151	2	13
β-strand	154-155	2	13
β-strand	160-164	5	12
α-helix	165-168	4
β-strand	175-183	9	12
α-helix	184-187	4
β-strand	193-197	5	14
β-strand	202	1	7
β-strand	206-210	5	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)
synthetic octapeptide WEHI 1886493	P	protein	7	synthetic construct

Sequence of entity 1 (H), FASTA

>7ZLJ_1 CMT2-Fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSSSVYWSWWGYSAFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (K), FASTA

>7ZLJ_2 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Sequence of entity 3 (L), FASTA

>7ZLJ_3 CMT2-Fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQGASEPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (A), FASTA

>7ZLJ_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

>7ZLJ_5 synthetic octapeptide WEHI 1886493 (chains P)
GSWAKWS

Ligands and cofactors

ID	Name	Formula	Copies
IZU	[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-y…	C32 H57 O8 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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