PDB-6wzz: GID4 in complex with VGLWKS peptide

ID or keywords:

Entry

Database: PDB / ID: 6wzz

Title

GID4 in complex with VGLWKS peptide

Components

Glucose-induced degradation protein 4 homolog
VGLWKS peptide

Keywords

PEPTIDE BINDING PROTEIN / GID4 / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosol / Glucose-induced degradation protein 4 homolog

Function and homology information

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Dong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Recognition of nonproline N-terminal residues by the Pro/N-degron pathway.
Authors: Dong, C. / Chen, S.J. / Melnykov, A. / Weirich, S. / Sun, K. / Jeltsch, A. / Varshavsky, A. / Min, J.

History

Deposition	May 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 8, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wzz.cif.gz	81.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6wzz.ent.gz	57.5 KB	Display	PDB format
PDBx/mmJSON format	6wzz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6wzz_validation.pdf.gz	424 KB	Display	wwPDB validaton report
Full document	6wzz_full_validation.pdf.gz	424.1 KB	Display
Data in XML	6wzz_validation.xml.gz	9 KB	Display
Data in CIF	6wzz_validation.cif.gz	11.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wz/6wzz ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wzz	HTTPS FTP

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Related structure data

Related structure data	6wzxC 6ccrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6cdg-d 6cd9-d 6wzx-1 5jly-3 3k7g-d 3f59-1 3p2a-4 6wzx-2 3suf-4 3f59-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glucose-induced degradation protein 4 homolog

B: VGLWKS peptide

20.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	36.781, 40.648, 56.319
Angle α, β, γ (deg.)	90.000, 98.102, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog Mass: 19604.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V3R / References: UniProt: Q8IVV7
#2: Protein/peptide	VGLWKS peptide Mass: 689.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 13 / Source method: obtained synthetically
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.11 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.03 M Citric acid, pH 7.6 and 20% (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97625 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 1.6→40.65 Å / Num. obs: 21226 / % possible obs: 96.3 % / Redundancy: 3.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.047 / R_pim(I) all: 0.031 / R_rim(I) all: 0.056 / Net I/σ(I): 13.8 / Num. measured all: 65453 / Scaling rejects: 3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.6-1.62	1.7	0.588	1291	746	0.658	0.518	0.787	1.3	68.5
8.75-40.65	3	0.03	461	153	0.998	0.02	0.036	37.5	98.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.4	data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr

Resolution: 1.6→36.403 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.948 / SU B: 2.208 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2197	1049	4.956 %
R_work	0.1856	20116	-
all	0.187	-	-
obs	-	21165	96.481 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 21.394 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.735 Å²	0 Å²	-0.739 Å²
2-	-	-0.593 Å²	0 Å²
3-	-	-	0.065 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→36.403 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1353	0	13	50	1416

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1446
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1236
X-RAY DIFFRACTION	r_angle_refined_deg	1.67	1.638	1968
X-RAY DIFFRACTION	r_angle_other_deg	1.458	1.578	2866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.805	5	177
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.43	23.377	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.812	15	225
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.686	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	176
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1651
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	346
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	260
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	1114
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	679
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	641
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	48
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.141	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.142	0.2	29
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.116	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.985	2.226	677
X-RAY DIFFRACTION	r_mcbond_other	1.984	2.226	677
X-RAY DIFFRACTION	r_mcangle_it	2.998	3.325	845
X-RAY DIFFRACTION	r_mcangle_other	2.997	3.328	846
X-RAY DIFFRACTION	r_scbond_it	2.576	2.401	769
X-RAY DIFFRACTION	r_scbond_other	2.575	2.403	770
X-RAY DIFFRACTION	r_scangle_it	3.836	3.524	1117
X-RAY DIFFRACTION	r_scangle_other	3.835	3.526	1118
X-RAY DIFFRACTION	r_lrange_it	5.03	24.55	1619
X-RAY DIFFRACTION	r_lrange_other	5.015	24.398	1606

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.6-1.642	0.249	44	0.29	1157	0.288	1596	0.809	0.785	75.2506	0.275
1.642-1.686	0.273	68	0.262	1280	0.262	1582	0.789	0.817	85.2086	0.238
1.686-1.735	0.278	87	0.243	1362	0.245	1515	0.835	0.849	95.6436	0.22
1.735-1.789	0.262	75	0.225	1400	0.227	1486	0.888	0.874	99.2598	0.197
1.789-1.847	0.28	71	0.209	1355	0.212	1430	0.881	0.908	99.7203	0.181
1.847-1.912	0.247	72	0.185	1316	0.188	1392	0.92	0.933	99.7126	0.16
1.912-1.984	0.176	67	0.175	1255	0.175	1331	0.937	0.943	99.3238	0.154
1.984-2.064	0.217	71	0.185	1225	0.187	1300	0.926	0.938	99.6923	0.164
2.064-2.156	0.252	55	0.19	1185	0.193	1245	0.917	0.937	99.5984	0.171
2.156-2.261	0.227	52	0.177	1126	0.179	1181	0.938	0.947	99.746	0.157
2.261-2.382	0.157	47	0.17	1085	0.169	1136	0.963	0.954	99.6479	0.155
2.382-2.526	0.189	52	0.174	1008	0.174	1064	0.951	0.952	99.6241	0.163
2.526-2.7	0.268	50	0.189	970	0.193	1021	0.925	0.946	99.9021	0.177
2.7-2.915	0.214	52	0.182	884	0.184	940	0.942	0.946	99.5745	0.177
2.915-3.191	0.239	51	0.174	816	0.177	872	0.946	0.954	99.4266	0.178
3.191-3.564	0.274	36	0.177	745	0.18	787	0.927	0.96	99.2376	0.186
3.564-4.109	0.178	44	0.154	668	0.156	715	0.954	0.966	99.5804	0.17
4.109-5.016	0.157	26	0.146	558	0.146	587	0.972	0.972	99.4889	0.172
5.016-7.028	0.217	24	0.221	448	0.221	475	0.939	0.947	99.3684	0.245
7.028-36.403	0.335	5	0.253	273	0.254	280	0.903	0.924	99.2857	0.308

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