7PYV: Human UBA6

Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10. Determined by X-ray diffraction at 3.27 Å resolution. Released 24 Aug 2022.

Method: X-ray diffraction
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 3
Atoms: 16,503
Mol. weight: 251.38 kDa
Released: 24 Aug 2022

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

Secondary structure: helices and β-sheets

7PYV contains 114 α-helices and 110 β-strands across 3 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: 56 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	55-61	7
β-strand	63-67	5	1
α-helix	71-83	13
β-strand	87-91	5	1
β-strand	95	1	2
α-helix	96	1
α-helix	100-103	4
α-helix	109-114	6
β-strand	117	1	2
α-helix	118-129	12
β-strand	134-138	5	1
α-helix	148-153	6
β-strand	156-159	4	1
α-helix	164-176	13
α-helix	180-181	2
β-strand	182-189	8	1
β-strand	190	1	3
β-strand	192-198	7	1
β-strand	203-205	3	4
α-helix	211-214	4
β-strand	215-217	3	5
β-strand	218-221	4	6
β-strand	228-231	4	6
β-strand	244-250	7	5
α-helix	254-258	5
β-strand	259-262	4	5
β-strand	264	1	6
β-strand	270-272	3	6
α-helix	280-282	3
β-strand	285-290	6	5
α-helix	291-292	2
β-strand	295-297	3	4
α-helix	302-307	6
β-strand	311	1	1
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	373-382	10
β-strand	386	1	3
α-helix	388-407	20
β-strand	416-417	2	1
β-strand	420	1	1
α-helix	422-425	4
α-helix	426-428	3
α-helix	433-436	4
α-helix	444-459	16
β-strand	463-466	4	7
α-helix	470-482	13
β-strand	493-496	4	7
β-strand	500	1	8
α-helix	514-516	3
β-strand	520	1	8
α-helix	521-532	12
β-strand	538-541	4	7
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	7
α-helix	571-584	14
β-strand	588-594	7	7
β-strand	597-603	7	7
β-strand	608	1	9
α-helix	612-614	3
α-helix	617-622	6
α-helix	626-629	4
α-helix	634-649	16
α-helix	651-661	11
α-helix	665-671	7
α-helix	677-685	9
α-helix	686-690	5
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727-728	2	10
β-strand	732-733	2	10
α-helix	752-769	18
α-helix	777-786	10
α-helix	790-792	3
α-helix	824-832	9
α-helix	834-835	2
α-helix	836-838	3
α-helix	854-856	3
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-888	9
α-helix	895-914	20
β-strand	922-927	6	7
β-strand	932-937	6	7
α-helix	938-939	2
β-strand	940	1	9
α-helix	941	1
β-strand	944	1	11
β-strand	952	1	11
β-strand	958-961	4	12
β-strand	967	1	13
α-helix	968-979	12
β-strand	985-987	3	14
β-strand	994	1	14
α-helix	1001-1006	6
β-strand	1008	1	13
α-helix	1009-1012	4
β-strand	1021-1024	4	12
β-strand	1025-1028	4	14
β-strand	1038-1039	2	14
β-strand	1043-1046	4	12

Chain B: 54 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	55-61	7
β-strand	63-67	5	18
α-helix	71-83	13
β-strand	87-91	5	18
β-strand	95	1	19
α-helix	96	1
α-helix	100-103	4
α-helix	109-114	6
β-strand	117	1	19
α-helix	118-129	12
β-strand	134-138	5	18
α-helix	148-153	6
β-strand	156-159	4	18
α-helix	164-176	13
α-helix	180-181	2
β-strand	182-189	8	18
β-strand	190	1	20
β-strand	192-198	7	18
β-strand	203-205	3	21
α-helix	211-214	4
β-strand	215-217	3	22
β-strand	218-221	4	23
β-strand	228-231	4	23
β-strand	244-250	7	22
α-helix	254-258	5
β-strand	259-262	4	22
β-strand	264	1	23
β-strand	270-272	3	23
α-helix	280-282	3
β-strand	285-290	6	22
α-helix	291-292	2
β-strand	295-297	3	21
α-helix	302-307	6
β-strand	311	1	18
α-helix	321-339	19
α-helix	342-344	3
α-helix	348-364	17
α-helix	373-382	10
β-strand	386	1	20
α-helix	388-407	20
β-strand	416-417	2	18
β-strand	420	1	18
α-helix	422-425	4
α-helix	426-428	3
α-helix	433-436	4
α-helix	444-459	16
β-strand	463-466	4	24
α-helix	470-482	13
β-strand	493-496	4	24
β-strand	500	1	25
α-helix	514-516	3
β-strand	520	1	25
α-helix	521-532	12
β-strand	538-541	4	24
α-helix	547-549	3
α-helix	555-560	6
β-strand	563-566	4	24
α-helix	571-584	14
β-strand	588-594	7	24
β-strand	597-603	7	24
β-strand	608	1	26
α-helix	612-614	3
α-helix	626-629	4
α-helix	634-649	16
α-helix	651-661	11
α-helix	665-671	7
α-helix	677-685	9
α-helix	686-690	5
α-helix	696-708	13
α-helix	709-713	5
α-helix	714-721	8
β-strand	727-728	2	27
β-strand	732-733	2	27
α-helix	752-769	18
α-helix	777-786	10
α-helix	822-832	11
α-helix	834-835	2
α-helix	836-838	3
α-helix	854-856	3
α-helix	858-872	15
α-helix	875-877	3
α-helix	880-888	9
α-helix	895-914	20
β-strand	922-927	6	24
β-strand	932-937	6	24
α-helix	938-939	2
β-strand	940	1	26
α-helix	941	1
β-strand	944	1	28
β-strand	952	1	28
β-strand	958-961	4	29
β-strand	967	1	30
α-helix	968-979	12
β-strand	985-987	3	31
β-strand	994	1	31
α-helix	1001-1006	6
β-strand	1008	1	30
α-helix	1009-1012	4
β-strand	1021-1024	4	29
β-strand	1025-1028	4	31
β-strand	1038-1039	2	31
β-strand	1043-1046	4	29

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	15
β-strand	20-24	5	15
β-strand	29	1	16
α-helix	30-40	11
β-strand	48-52	5	15
β-strand	55-56	2	15
β-strand	62	1	16
α-helix	64-66	3
β-strand	73-80	8	15
β-strand	89-95	7	7
β-strand	102-107	6	7
β-strand	111	1	17
α-helix	112-123	12
β-strand	132-134	3	7
β-strand	137-138	2	7
β-strand	144	1	17
α-helix	145-148	4
β-strand	155-158	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme…	A, B	protein	1045	Homo sapiens	A0AVT1 (AlphaFold model), P22314 (AlphaFold model)
UBD	C	protein	159	Homo sapiens	O15205 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PYV_1 Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6 (chains A, B)
MEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMA
KSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAE
AVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPP
IKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLE
TGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFE
SLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATS
ISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLE
AADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFA
LLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDA
HLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHT
EVIVPHLTESYNSHRDPPEEEIPIATLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYL
TDPKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWADCVTWACHHWHTQYSNNIRQLLH
NFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDRAAV
ATFLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLPGFKMYPI
DFEKDDDSNFHMDFIVAASNLRAENYDIPSADRHKSKLIAGKIIPAIATTTATVSGLVAL
EMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFT
LLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVS
FAPDIDGDEDLPGPPVRYYFSHDTD

Sequence of entity 2 (C), FASTA

>7PYV_2 UBD (chains C)
TLTVHVRSEEWDLMTFDANPYDSVKKIKEHVRSKTKVPVQDQVLLLGSKILKPRRSLSSY
GIDKEKTIHLTLKVVKPSDEELPLFLVESGDEAKRHLLQVRRSSSVAQVKAMIETKTGII
PETQIVTLNGKRLEDGKMMADYGIRKGNLLFLASYSIGG

Primary citation

Structures of UBA6 explain its dual specificity for ubiquitin and FAT10. Truongvan, N., Li, S., Misra, M. et al. Nat Commun (2022) 13:4789-4789. DOI 10.1038/s41467-022-32040-6 · PubMed

Other PDB entries of the same protein (UniProt A0AVT1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SOL 2.25 Å, Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6
7PVN 2.71 Å, Crystal Structure of Human UBA6 in Complex with ATP
9YKV 2.73 Å, Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic…
28MJ 2.77 Å, Cryo-EM structure of UBA6 in complex with FAT10 in the pre-adenylation state.
28MO 3.01 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (singly loaded)
28MQ 3.04 Å, Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex
9QH5 3.09 Å, Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded)
28MP 3.12 Å, Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
9YLF 3.14 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/Ub(a) adenylate complex.
9YLB 3.24 Å, Cryo-EM structure of single-loaded human UBA6-UBE2Z/FAT10(a) adenylate complex.
9QIC 3.29 Å, Consensus structure of UBA6
9XGB 3.3 Å, UBA6-BIRC6 ubc-ubt

Browse structure collections

About this viewer

MolViewer shows 7PYV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.