PDB-5hqp: Crystal structure of the ERp44-peroxiredoxin 4 complex

ID or keywords:

Entry

Database: PDB / ID: 5hqp

Title

Crystal structure of the ERp44-peroxiredoxin 4 complex

Components

Endoplasmic reticulum resident protein 44
Peroxiredoxin-4

Keywords

OXIDOREDUCTASE/CHAPERONE /

CHAPERONE / GST fold /

OXIDOREDUCTASE / beta/alpha/beta sandwich / OXIDOREDUCTASE-CHAPERONE complex

Function / homology

Function and homology information

cellular response to stress / glycoprotein metabolic process / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding /

protein disulfide isomerase activity /

endoplasmic reticulum-Golgi intermediate compartment ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Yang, K. / Li, D.F. / Wang, X. / Wang, C.C.

Citation

Journal: Structure / Year: 2016
Title: Crystal Structure of the ERp44-Peroxiredoxin 4 Complex Reveals the Molecular Mechanisms of Thiol-Mediated Protein Retention.
Authors: Yang, K. / Li, D.F. / Wang, X. / Liang, J. / Sitia, R. / Wang, C.C. / Wang, X.

History

Deposition	Jan 22, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5hqp.cif.gz	385.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5hqp.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	5hqp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	2r2jS 3tjgS 3tkp S: Starting model for refinement
Similar structure data	3o3n-d 5f8e-d 2ix8-d 3syn-d 1b70-d 3o3m-d 5if0-d 6bmv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1)

Deposited unit

A: Peroxiredoxin-4

B: Peroxiredoxin-4

C: Endoplasmic reticulum resident protein 44

D: Endoplasmic reticulum resident protein 44

144 kDa, 4 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)	69.289, 198.979, 225.959
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Peroxiredoxin-4 / / Antioxidant enzyme AOE372 / AOE37-2 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / ...Antioxidant enzyme AOE372 / AOE37-2 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372 Mass: 28007.484 Da / Num. of mol.: 2 / Mutation: T118E, C14S, C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13162, peroxiredoxin
#2: Protein	Endoplasmic reticulum resident protein 44 / ERp44 / Thioredoxin domain-containing protein 4 Mass: 44185.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERP44, KIAA0573, TXNDC4, UNQ532/PRO1075 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BS26
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.39 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1mM MES (pH5.6), 16% PEG 400 / PH range: 5.6-6.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 31, 2015
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 2.6→99.49 Å / Num. all: 48595 / Num. obs: 48595 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / R_merge(I) obs: 0.084 / R_sym value: 0.084 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 9.2 % / R_merge(I) obs: 0.85 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2R2J, 3TJG

2r2j

3tjg

Resolution: 2.6→49.745 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2717	2369	4.89 %	Random
R_work	0.2347	-	-	-
obs	0.2366	48461	99.81 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→49.745 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7192	0	0	27	7219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7362
X-RAY DIFFRACTION	f_angle_d	1.301	9965
X-RAY DIFFRACTION	f_dihedral_angle_d	18.609	4416
X-RAY DIFFRACTION	f_chiral_restr	0.073	1078
X-RAY DIFFRACTION	f_plane_restr	0.007	1300

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.6531	0.4051	137	0.3614	2691	X-RAY DIFFRACTION	100
2.6531-2.7108	0.3473	142	0.3312	2642	X-RAY DIFFRACTION	99
2.7108-2.7738	0.3663	130	0.3182	2705	X-RAY DIFFRACTION	100
2.7738-2.8432	0.3757	147	0.3111	2646	X-RAY DIFFRACTION	100
2.8432-2.92	0.3818	138	0.2911	2677	X-RAY DIFFRACTION	100
2.92-3.006	0.3171	136	0.2779	2705	X-RAY DIFFRACTION	100
3.006-3.103	0.3151	124	0.2691	2673	X-RAY DIFFRACTION	100
3.103-3.2139	0.2683	114	0.2537	2699	X-RAY DIFFRACTION	100
3.2139-3.3425	0.2776	132	0.2672	2714	X-RAY DIFFRACTION	100
3.3425-3.4946	0.272	158	0.2585	2683	X-RAY DIFFRACTION	100
3.4946-3.6788	0.2553	142	0.2321	2703	X-RAY DIFFRACTION	100
3.6788-3.9092	0.2865	142	0.229	2717	X-RAY DIFFRACTION	100
3.9092-4.2109	0.2464	123	0.2124	2723	X-RAY DIFFRACTION	100
4.2109-4.6344	0.2586	153	0.1859	2731	X-RAY DIFFRACTION	100
4.6344-5.3043	0.2301	146	0.1899	2736	X-RAY DIFFRACTION	100
5.3043-6.6803	0.2627	149	0.2412	2764	X-RAY DIFFRACTION	100
6.6803-49.7538	0.2605	156	0.2318	2883	X-RAY DIFFRACTION	100

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	2.4128	-1.2004	-0.5907	1.712	-0.2397	2.9145	0.0641	0.5369	0.2094	-0.1745	0.0746	-0.1991	-0.0917	0.3506	-0.0002	0.4748	-0.0581	0.0727	0.7381	0.0213	0.598	46.431	95.5904	76.2347
2	0.0199	0.0082	-0.858	2.4571	-0.5799	1.6663	-0.1971	0.4356	-0.0619	-0.286	-0.0212	0.1687	0.3537	-0.2178	-0.0011	0.7381	-0.039	0.0681	0.8231	-0.055	0.4959	38.4409	89.2267	73.1527
3	0.8441	-0.4841	-0.1404	2.4106	-0.9078	2.6443	-0.2055	0.596	-0.0815	-0.105	0.0651	-0.1748	0.5805	0.3454	-0.0027	0.5977	-0.0049	0.093	0.8689	-0.0187	0.5809	48.7293	89.2527	76.9718
4	0.4388	0.0374	0.2228	-0.0801	0.2879	0.748	-0.0231	0.1966	-0.3714	0.0148	0.089	0.4674	0.2498	-0.6059	-0.0011	0.5591	-0.1566	0.0185	0.7102	0.028	0.5874	29.3661	93.0121	84.8524
5	1.0108	-0.156	-0.2391	0.0947	-0.116	0.5771	0.2535	0.7299	0.1802	-0.9462	0.5283	0.3275	0.2878	0.5856	0	0.7783	-0.048	-0.0537	0.9495	-0.0233	0.7566	20.5036	91.4416	94.8031
6	0.0702	0.373	-0.15	0.3106	-0.1671	0.1881	-0.3013	-0.237	-0.0364	0.4192	0.1393	-0.2891	-0.1157	0.6567	-0.0034	0.6977	0.1176	0.0583	0.8751	0.0031	0.7979	52.0854	86.2506	100.4438
7	1.7149	0.2237	-1.5566	0.704	0.0719	2.2139	0.0122	-0.4236	-0.1101	0.1561	-0.0138	0.1004	0.519	0.3217	0.0001	0.6626	0.0613	-0.005	0.552	0.0627	0.5102	38.2344	84.3817	108.2226
8	0.276	-0.1313	0.173	0.1084	0.344	0.4103	-0.4193	-0.3931	-0.8355	0.3073	0.587	0.0964	0.6958	-0.8141	-0.0024	0.8727	-0.1266	0.1778	0.4407	0.024	0.7354	30.1095	77.4968	100.4127
9	-0.0244	0.2949	0.0642	0.7002	-0.6806	0.6167	0.0478	-0.2256	-0.1494	0.1294	-0.2506	-0.3394	-0.0524	0.2703	-0.0003	0.6502	0.001	0.0722	0.5082	0.0235	0.6246	34.2497	87.1714	111.4217
10	0.8314	0.647	-0.1681	0.4691	0.1843	1.8209	0.0362	0.5786	-0.2548	-0.1355	0.1151	0.2419	0.8207	-1.8305	0.0081	0.7474	-0.0685	0.1548	0.6891	0.1157	0.6852	23.1534	86.8847	109.8522
11	0.239	-0.1945	-0.0696	0.0314	-0.0542	0.1076	0.1601	-0.2746	-0.6237	0.7472	-0.2212	-0.7541	-0.266	0.6593	0.0008	0.5785	0.0307	0.0019	0.6712	0.042	0.6781	44.1172	91.7208	109.2728
12	0.117	-0.1085	0.1537	0.2804	0.3842	0.4956	-0.2331	0.2248	-0.0035	-0.737	0.2118	0.0275	-0.5711	1.2169	0.0008	0.6115	-0.0713	-0.059	0.6525	0.068	0.592	42.7245	98.6389	102.4
13	1.9366	1.7252	0.838	1.3306	0.5468	0.5265	-0.3184	-0.1051	0.046	-0.1624	0.1992	0.3282	0.55	-0.5384	0.0013	0.585	0.0892	0.0758	0.6425	0.0705	0.5432	41.0447	85.3617	95.7563
14	-0.0108	0.4044	0.1738	0.3566	0.1957	0.3613	-0.0809	0.4082	-0.0918	-0.1822	0.3542	0.1067	0.5895	0.4359	-0.0033	0.9855	0.007	0.1295	0.6296	-0.1257	0.7406	41.747	72.6486	85.8851
15	4.5627	-1.4626	1.5819	5.9943	-0.3309	2.8407	-0.1908	-0.6821	0.0684	0.043	0.0266	0.5075	-0.1249	-0.4133	-0.0003	0.4773	-0.026	-0.0029	0.7245	-0.0262	0.5728	5.7055	103.8078	98.9191
16	0.9675	-0.1485	-0.1142	1.4367	1.0571	0.6533	-0.779	0.8326	0.861	-0.819	0.3951	-0.5963	-2.1234	0.5848	-0.0059	1.6812	-0.0851	-0.1845	0.7136	0.2584	1.1499	3.2767	122.7468	82.0857
17	1.3539	0.5531	0.068	1.7767	-0.1366	0.1955	0.0275	0.63	0.5143	-0.8518	0.1724	0.4693	0.0686	-0.9266	0.0017	1.1745	0.0841	-0.2339	0.7955	0.1487	1.1818	-7.5537	117.8548	76.5116
18	2.7379	-0.205	0.4774	4.3914	-0.7265	6.8473	-0.053	-0.4885	-0.0796	0.5532	0.092	-0.5936	0.5571	1.6202	0.0001	0.6175	0.1354	-0.0517	1.3712	-0.0184	0.6137	8.6939	91.7874	69.3283
19	2.5225	1.2438	-1.6569	0.8299	-0.921	1.0398	1.0441	0.3758	-0.2044	0.6078	-0.9793	0.6631	0.4268	-0.9634	0.0066	3.5223	-0.1762	0.2225	1.7579	-0.74	2.3455	46.7718	49.7557	62.1625
20	0.0417	0.0916	-0.573	0.5033	-0.0769	0.1398	-0.3377	0.1154	-0.3329	-1.8812	-0.108	-1.0354	0.7721	0.4865	-0.003	1.9	0.2165	0.4963	1.1173	-0.2092	1.5654	54.6953	58.0571	68.0845
21	0.6188	0.6936	-0.0449	2.4574	0.5382	2.0549	-0.1198	0.0117	-0.2569	0.0734	0.1166	0.2858	0.5539	-0.6394	-0.002	1.4103	-0.1206	0.2998	0.8474	-0.1657	1.6298	52.9111	46.1297	81.4467
22	1.4579	-0.3685	-0.4069	0.397	-0.2005	0.1544	-0.0778	0.3802	0.7106	-0.0781	-0.1827	-1.7331	0.4373	-0.2172	-0.0045	1.6773	-0.0721	0.1657	0.9384	-0.0317	2.3977	48.6967	29.5314	83.4909

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 76 through 125 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 126 through 152 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 153 through 224 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 225 through 240 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 241 through 256 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 76 through 88 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 89 through 125 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 126 through 141 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 142 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 174 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 175 through 187 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 188 through 199 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 200 through 224 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 225 through 250 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 99 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 100 through 132 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 133 through 212 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 213 through 331 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 2 through 18 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 19 through 67 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 68 through 135 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 136 through 213 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi