PDB-5nkz: Crystal structure of H. polymorpha ubiquitin conjugating enzyme P...

ID or keywords:

Entry

Database: PDB / ID: 5nkz

Title

Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p

Components

Peroxin 22
Ubiquitin-conjugating enzyme E2-21 kDa

Keywords

TRANSFERASE / Pex4 / Pex22 / Ubiquitin conjugating enzyme / Crystallization / Hansenula polymorpha / Peroxisome import

Function / homology

Function and homology information

peroxisome organization / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin-protein transferase activity / protein ubiquitination / ATP binding
Similarity search - Function

Biological species

Pichia angusta (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Danda, N. / Lunev, S. / Ali, A. / Groves, M.R. / Williams, C.

Funding support

Netherlands, Qatar, 2items

Citation

Journal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex.
Authors: Groves, M.R. / Schroer, C.F.E. / Middleton, A.J. / Lunev, S. / Danda, N. / Ali, A.M. / Marrink, S.J. / Williams, C.

History

Deposition	Apr 3, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Jan 17, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5nkz.cif.gz	247.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5nkz.ent.gz	200.9 KB	Display	PDB format
PDBx/mmJSON format	5nkz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/5nkz ftp://data.pdbj.org/pub/pdb/validation_reports/nk/5nkz	HTTPS FTP

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Related structure data

Related structure data	5nl8C 2y9mS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2i1l-1 5c1s-2 4mcj-3 4cim-d 6dwu-33 2i1l-2 1s4m-2 3lid-1 6dwf-1 3q0d-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (7) #60 - Dec 2004 Ubiquitin similarity (7)

Deposited unit

A: Ubiquitin-conjugating enzyme E2-21 kDa

D: Peroxin 22

C: Peroxin 22

B: Ubiquitin-conjugating enzyme E2-21 kDa

74.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin-conjugating enzyme E2-21 kDa

C: Peroxin 22

defined by software
Evidence: light scattering, 1:1 interaction stoichiometry of the Pex22S:Pex4p complex in vitro was confirmed by SLS analysis.
37.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Peroxin 22

B: Ubiquitin-conjugating enzyme E2-21 kDa

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

Unit cell

Length a, b, c (Å)	44.683, 61.582, 78.441
Angle α, β, γ (deg.)	89.18, 78.02, 84.09
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	D
2	2	C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	TYR	TYR	A	A	2 - 183	4 - 185
2	1	ALA	ALA	TYR	TYR	B	D	2 - 183	4 - 185
1	2	GLY	GLY	VAL	VAL	D	B	51 - 153	29 - 131
2	2	GLY	GLY	VAL	VAL	C	C	51 - 153	29 - 131

NCS ensembles :

ID
1
2

#1: Protein	Ubiquitin-conjugating enzyme E2-21 kDa / E2 ubiquitin-conjugating enzyme PEX4 / Peroxin-4 / Ubiquitin carrier protein / Ubiquitin-protein ligase Mass: 21671.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pichia angusta (fungus) / Gene: PEX4 / Production host: Escherichia coli (E. coli) References: UniProt: O60015, E2 ubiquitin-conjugating enzyme
#2: Protein	Peroxin 22 Mass: 15625.518 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pichia angusta (fungus) / Gene: PEX22 / Production host: Escherichia coli (E. coli) / References: UniProt: A2T0X6

#1: Protein

Ubiquitin-conjugating enzyme E2-21 kDa / E2 ubiquitin-conjugating enzyme PEX4 / Peroxin-4 / Ubiquitin carrier protein / Ubiquitin-protein ligase

Mass: 21671.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pichia angusta (fungus) / Gene: PEX4 / Production host:

Escherichia coli (E. coli)
References: UniProt: O60015, E2 ubiquitin-conjugating enzyme

#2: Protein

Peroxin 22

Mass: 15625.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pichia angusta (fungus) / Gene: PEX22 / Production host:

Escherichia coli (E. coli) / References: UniProt: A2T0X6

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M BIS-TRIS Propane pH 7.8, 0.2 M sodium sulphate, 22 % w/v PEG-3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.85→48.0397 Å / Num. obs: 20450 / % possible obs: 95.02 % / Redundancy: 3.93 % / R_merge(I) obs: 0.123 / Net I/σ(I): 6.03
Reflection shell	Resolution: 2.85→2.95 Å / Redundancy: 5.49 % / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 1822 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
MOLREP		phasing
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Pex4:Pex22 complex coordinates from S. cerevisae (PDB: 2Y9M(Williams et al. 2012); 33/57 % and 14/35 % identity/similarity, respectively) as starting model

2y9m

Resolution: 2.85→48.0397 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.892 / SU B: 60.112 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2837	980	5 %	RANDOM
R_work	0.23608	-	-	-
obs	0.2385	18451	95.02 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 74.337 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.85 Å²	-0.04 Å²	-2.49 Å²
2-	-	-0.81 Å²	5.69 Å²
3-	-	-	-3.15 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→48.0397 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4639	0	0	0	4639

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	4763
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4469
X-RAY DIFFRACTION	r_angle_refined_deg	1.925	1.965	6471
X-RAY DIFFRACTION	r_angle_other_deg	1.158	3	10408
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.281	5	574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.019	24.727	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.173	15	848
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.592	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	740
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	5181
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	918
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.327	4.493	2302
X-RAY DIFFRACTION	r_mcbond_other	2.326	4.492	2301
X-RAY DIFFRACTION	r_mcangle_it	3.826	6.733	2874
X-RAY DIFFRACTION	r_mcangle_other	3.825	6.734	2875
X-RAY DIFFRACTION	r_scbond_it	2.141	4.693	2461
X-RAY DIFFRACTION	r_scbond_other	2.14	4.693	2462
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.657	6.943	3598
X-RAY DIFFRACTION	r_long_range_B_refined	6.058	52.633	5316
X-RAY DIFFRACTION	r_long_range_B_other	6.058	52.63	5317
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11432	0.1
1	2	B	11432	0.1
2	1	D	6186	0.12
2	2	C	6186	0.12

LS refinement shell

Resolution: 2.78→2.852 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.476	64	-
R_work	0.453	1222	-
obs	-	-	87.48 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.9994	-0.0512	-0.359	3.3485	-0.431	7.4353	-0.2284	0.4925	0.5508	-0.1938	0.0978	0.1426	-0.3797	-0.2543	0.1306	0.0916	-0.0346	-0.0011	0.1456	-0.1002	0.3438	-1.3187	27.0794	10.7215
2	1.5976	0.8038	-0.1246	2.4018	1.7813	6.1136	-0.0764	-0.3244	0.1822	0.0267	0.2243	0.0151	-0.1484	0.2388	-0.1478	0.043	-0.0244	0.0861	0.2832	-0.2668	0.3648	8.1971	25.7731	22.7209
3	4.1447	-2.4763	0.1534	3.8058	0.433	6.8617	0.3215	0.8453	0.7242	-0.5048	-0.3075	0.1681	-0.5254	-0.7798	-0.014	0.2413	0.015	0.0404	0.5316	-0.0654	0.653	-8.5157	10.2549	-3.2462
4	3.4337	-2.6714	-3.7216	7.2919	-0.1533	6.1191	-0.4633	0.0981	-0.4257	-0.0603	0.0683	0.6473	0.6046	-0.1832	0.395	0.1589	-0.0525	-0.0029	0.21	-0.1865	0.2956	-2.8913	2.6149	2.3558
5	2.1086	1.3569	2.1598	5.5217	4.2636	7.3715	0.0951	0.1898	-0.1798	-0.1322	0.0848	0.3654	0.3659	-0.2186	-0.1799	0.1471	-0.0623	0.0702	0.1982	-0.1307	0.3684	-1.3249	-9.8157	-5.0388
6	6.3252	-4.8482	-3.1417	6.5131	3.418	1.9252	-0.1487	-0.2829	0.0443	0.3052	0.1641	0.0506	0.1373	0.1329	-0.0154	0.0384	-0.0571	0.0837	0.1891	-0.2316	0.2996	2.2283	6.6435	7.1187
7	6.5754	-1.2169	0.9867	4.3356	-0.8886	0.942	0.1897	0.1561	-0.1805	0.1163	-0.0757	-0.0018	0.2513	0.2755	-0.114	0.1994	-0.0054	0.0894	0.1926	-0.1725	0.198	12.1947	-9.1466	-0.2209
8	5.1964	4.919	-5.8426	12.759	-9.7855	22.0142	-0.0108	0.1989	0.093	0.4747	0.363	0.3047	0.1391	-0.1222	-0.3522	0.0771	0.0534	-0.009	0.2784	-0.178	0.2022	13.8793	32.5933	49.0897
9	14.5877	-4.0007	1.3839	1.5444	0.5352	7.4085	-0.4703	-0.2179	-0.7032	0.1283	0.156	-0.171	0.2642	0.0357	0.3143	0.2902	-0.028	0.0713	0.201	-0.1159	0.5676	9.7431	36.1537	54.9576
10	5.2609	-2.5773	-2.6877	5.037	1.203	6.4171	-0.1771	-0.1951	-0.0257	0.383	0.2099	0.0205	0.1447	0.0523	-0.0328	0.1922	-0.017	0.0045	0.2955	-0.2456	0.219	7.7596	29.4849	46.0633
11	1.332	0.7294	-2.7449	10.8487	-7.9727	9.7579	-0.0633	-0.2187	-0.1576	-0.1448	-0.0627	0.19	0.3738	0.3914	0.1261	0.3049	-0.0102	-0.0009	0.4568	-0.231	0.5048	19.8009	28.3796	49.0955
12	1.178	-2.9887	-0.5251	8.6639	0.0901	1.7583	-0.0553	-0.1275	0.073	0.1219	0.1149	-0.2546	-0.0422	0.1967	-0.0597	0.2876	-0.0637	-0.0448	0.48	-0.0245	0.4457	23.8819	31.3111	46.9672
13	4.8403	1.4511	-1.7099	5.0375	0.1203	6.8981	-0.0219	0.2464	-0.1929	-0.0142	0.0558	0.1037	0.1096	0.0116	-0.0339	0.0799	-0.0297	0.0528	0.2011	-0.2418	0.3014	19.3708	-21.6337	-11.4643
14	8.091	0.6632	-0.4408	7.0418	-0.2495	0.0414	-0.216	-0.2198	-0.4182	0.2094	0.1866	-0.3026	-0.0306	0.0272	0.0294	0.1344	-0.0691	0.0583	0.22	-0.1965	0.2304	19.9376	-21.981	3.536
15	5.1227	-1.4738	-1.0998	4.3424	6.171	10.7803	0.0558	0.072	0.0662	0.5114	0.0357	-0.1967	1.1926	-0.3402	-0.0915	0.2283	-0.0249	-0.0446	0.2787	0.0209	0.3986	15.1591	-31.2415	0.1264

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 67
2	X-RAY DIFFRACTION	2	A	68 - 183
3	X-RAY DIFFRACTION	3	B	2 - 51
4	X-RAY DIFFRACTION	4	B	52 - 78
5	X-RAY DIFFRACTION	5	B	79 - 119
6	X-RAY DIFFRACTION	6	B	120 - 149
7	X-RAY DIFFRACTION	7	B	150 - 183
8	X-RAY DIFFRACTION	8	C	51 - 61
9	X-RAY DIFFRACTION	9	C	62 - 70
10	X-RAY DIFFRACTION	10	C	71 - 120
11	X-RAY DIFFRACTION	11	C	121 - 133
12	X-RAY DIFFRACTION	12	C	134 - 155
13	X-RAY DIFFRACTION	13	D	50 - 106
14	X-RAY DIFFRACTION	14	D	107 - 140
15	X-RAY DIFFRACTION	15	D	141 - 154

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