6JWI: Yeast Npl4

Yeast Npl4 in complex with Lys48-linked diubiquitin. Determined by X-ray diffraction at 2.55 Å resolution. Released 25 Dec 2019.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Mus musculus, Saccharomyces cerevisiae S288c
Chains: 4
Atoms: 9,116
Mol. weight: 131.65 kDa
Ligands: ZN, BCN
Released: 25 Dec 2019

Explore 6JWI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JWI contains 55 α-helices and 66 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: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	117-124	8
α-helix	128	1
β-strand	129	1	3
α-helix	130	1
α-helix	150	1
β-strand	151	1	3
α-helix	152	1
α-helix	156-161	6
β-strand	167-168	2	4
α-helix	169-180	12
β-strand	193	1	5
α-helix	209	1
α-helix	221-223	3
β-strand	224-226	3	6
β-strand	231-232	2	4
β-strand	236-239	4	7
α-helix	242-255	14
β-strand	260-270	11	7
β-strand	276-285	10	7
α-helix	286-287	2
β-strand	292	1	8
β-strand	295	1	8
α-helix	301-315	15
β-strand	320-328	9	7
β-strand	331	1	9
β-strand	339	1	9
α-helix	352-364	13
β-strand	366-368	3	10
β-strand	372	1	5
β-strand	376-379	4	10
β-strand	382-388	7	7
β-strand	394-401	8	7
α-helix	403-410	8
β-strand	414-416	3	11
β-strand	422-425	4	11
α-helix	426-428	3
β-strand	437-442	6	6
β-strand	448-452	5	6
β-strand	456-458	3	11
α-helix	459-462	4
β-strand	463-469	7	7
α-helix	476-477	2
α-helix	488-489	2
β-strand	492	1	12
α-helix	493-495	3
β-strand	497	1	12
α-helix	501-504	4
α-helix	505-509	5
α-helix	510-514	5
α-helix	517-524	8
α-helix	527-535	9
α-helix	541-552	12
α-helix	557-565	9
α-helix	567-579	13

Chain E: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	117-124	8
α-helix	128	1
β-strand	129	1	13
α-helix	130	1
α-helix	149-150	2
β-strand	151	1	13
α-helix	152	1
α-helix	156-161	6
β-strand	167-168	2	14
α-helix	169-180	12
β-strand	193	1	15
α-helix	209	1
α-helix	221-223	3
β-strand	224-226	3	16
β-strand	231-232	2	14
β-strand	236-239	4	17
α-helix	242-255	14
β-strand	260-270	11	17
β-strand	276-285	10	17
α-helix	286-288	3
β-strand	293	1	18
β-strand	295	1	18
α-helix	301-315	15
β-strand	320-328	9	17
β-strand	331	1	19
β-strand	339	1	19
α-helix	352-364	13
β-strand	366-368	3	20
β-strand	372	1	15
β-strand	376-379	4	20
β-strand	382-388	7	17
β-strand	394-401	8	17
α-helix	403-410	8
β-strand	414-416	3	21
β-strand	422-425	4	21
α-helix	426-428	3
β-strand	437-442	6	16
β-strand	448-452	5	16
β-strand	456-458	3	21
α-helix	459-462	4
β-strand	463-469	7	17
α-helix	488-489	2
α-helix	493-495	3
α-helix	501-504	4
α-helix	505-509	5
α-helix	510-514	5
α-helix	517-524	8
α-helix	527-535	9
α-helix	541-552	12
α-helix	557-565	9
α-helix	567-578	12

Chain G: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	22
β-strand	12-16	5	22
β-strand	22	1	23
α-helix	23-34	12
β-strand	42-45	4	22
β-strand	48-49	2	22
β-strand	55	1	23
β-strand	66-70	5	22

Chain I: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
β-strand	42-45	4	1
β-strand	48-49	2	1
β-strand	55	1	2
β-strand	66-70	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiqutin	G, I	protein	76	Mus musculus	P62984 (AlphaFold model)
Nuclear protein localization protein 4	A, E	protein	473	Saccharomyces cerevisiae S288c	P33755 (AlphaFold model)

Sequence of entity 1 (G, I), FASTA

>6JWI_1 Ubiqutin (chains G, I)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (A, E), FASTA

>6JWI_2 Nuclear protein localization protein 4 (chains A, E)
GPLGSIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHI
SFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQ
QQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEP
PQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDS
FFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEA
LVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLT
HGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNF
HLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
BCN	Bicine	C6 H13 N O4	9

Primary citation

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Sato, Y., Tsuchiya, H., Yamagata, A. et al. Nat Commun (2019) 10:5708-5708. DOI 10.1038/s41467-019-13697-y · PubMed

Other PDB entries of the same protein (UniProt P62984 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3AI5 1.4 Å, Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein
9H4N 2.46 Å, RPL13 (eL13)-mutant 80S ribosome from mouse
31FX 2.54 Å, Mouse 80S ribosome, sgRNA control
31FY 2.57 Å, Mouse 80S ribosome, Gm10076 KO
9KDT 2.63 Å, Cryo-EM structure of 80S ribosome
9KDW 2.67 Å, Cryo-EM structure of 80S ribosome
9QOH 2.78 Å, Mouse Ribosome POST translocation state
9QQP 2.8 Å, Mouse Ribosome rotated-2 PRE state
7CPU 2.82 Å, Cryo-EM structure of 80S ribosome from mouse kidney
31FZ 2.89 Å, Mouse 80S ribosome, eL41 KO
9KDU 2.96 Å, Cryo-EM structure of 80S ribosome
7CPV 3.03 Å, Cryo-EM structure of 80S ribosome from mouse testis

Browse structure collections

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