PDB-4xgu: Structure of C. elegans PCH-2

ID or keywords:

Entry

Database: PDB / ID: 4xgu

Title

Structure of C. elegans PCH-2

Components

Putative pachytene checkpoint protein 2

Keywords

ATP-binding protein / meiotic recombination / AAA+ ATPase / protein remodeler

Function / homology

Function and homology information

meiotic recombination checkpoint signaling / reciprocal meiotic recombination / kinetochore / chromosome / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.301 Å

Authors

Ye, Q. / Corbett, K.D.

Funding support

United States, 1items

Citation

Journal: Elife / Year: 2015
Title: TRIP13 is a protein-remodeling AAA+ ATPase that catalyzes MAD2 conformation switching.
Authors: Ye, Q. / Rosenberg, S.C. / Moeller, A. / Speir, J.A. / Su, T.Y. / Corbett, K.D.

History

Deposition	Jan 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2015	Group: Database references
Revision 1.2	Jun 3, 2015	Group: Database references
Revision 1.3	Jun 1, 2016	Group: Data collection
Revision 1.4	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xgu.cif.gz	904.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4xgu.ent.gz	762.3 KB	Display	PDB format
PDBx/mmJSON format	4xgu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgu ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgu	HTTPS FTP

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Related structure data

Similar structure data	21108 6r2e-d 3izg-d 3j7v-d 5uw6-d 5bof-1 6v8p-d 4ewj-1 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	#80 - Aug 2006 AAA+ Proteases similarity (2) #150 - Jun 2012 Sliding Clamps similarity (1) #166 - Oct 2013 Proteasome similarity (2) #167 - Nov 2013 SNARE Proteins similarity (2)

Deposited unit

A: Putative pachytene checkpoint protein 2

B: Putative pachytene checkpoint protein 2

C: Putative pachytene checkpoint protein 2

D: Putative pachytene checkpoint protein 2

E: Putative pachytene checkpoint protein 2

F: Putative pachytene checkpoint protein 2

hetero molecules

290 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Putative pachytene checkpoint protein 2

B: Putative pachytene checkpoint protein 2

C: Putative pachytene checkpoint protein 2

D: Putative pachytene checkpoint protein 2

E: Putative pachytene checkpoint protein 2

F: Putative pachytene checkpoint protein 2

hetero molecules

A: Putative pachytene checkpoint protein 2

B: Putative pachytene checkpoint protein 2

C: Putative pachytene checkpoint protein 2

D: Putative pachytene checkpoint protein 2

E: Putative pachytene checkpoint protein 2

F: Putative pachytene checkpoint protein 2

hetero molecules

defined by software
580 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.710, 240.970, 197.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Putative pachytene checkpoint protein 2 Mass: 48081.863 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pch-2, F10B5.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09535
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100 mM sodium citrate pH 5.6, 200 mM ammonium sulfate, 15% PEG 3350 PH range: 5.6

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Data collection

Diffraction	Mean temperature: 98 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2014
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.29→40 Å / Num. all: 134133 / Num. obs: 134133 / % possible obs: 99.5 % / Redundancy: 13.5 % / R_merge(I) obs: 0.098 / Net I/σ(I): 17.9
Reflection shell	Resolution: 2.29→2.33 Å / Redundancy: 10.6 % / R_merge(I) obs: 3.143 / Mean I/σ(I) obs: 0.8 / % possible all: 90.8

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
Aimless		data scaling
SHELX		phasing
RESOLVE		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.301→39.36 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 36.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.264	4884	5.08 %
R_work	0.2284	-	-
obs	0.2302	96084	71.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.301→39.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17851	0	89	55	17995

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	18202
X-RAY DIFFRACTION	f_angle_d	0.728	24601
X-RAY DIFFRACTION	f_dihedral_angle_d	15.094	6852
X-RAY DIFFRACTION	f_chiral_restr	0.027	2878
X-RAY DIFFRACTION	f_plane_restr	0.003	3130

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 (%)
2.3006-2.3268	0.7872	14	0.6596	266	X-RAY DIFFRACTION	6
2.3268-2.3541	0.5386	33	0.4585	815	X-RAY DIFFRACTION	19
2.3541-2.3828	0.5137	54	0.3996	1056	X-RAY DIFFRACTION	25
2.3828-2.413	0.4701	61	0.3692	1247	X-RAY DIFFRACTION	30
2.413-2.4448	0.3893	68	0.3852	1491	X-RAY DIFFRACTION	35
2.4448-2.4782	0.3673	89	0.3451	1678	X-RAY DIFFRACTION	40
2.4782-2.5136	0.3137	87	0.3216	1822	X-RAY DIFFRACTION	44
2.5136-2.5512	0.3597	119	0.3222	1986	X-RAY DIFFRACTION	47
2.5512-2.591	0.3522	130	0.3171	2161	X-RAY DIFFRACTION	52
2.591-2.6335	0.3378	126	0.3079	2336	X-RAY DIFFRACTION	56
2.6335-2.6789	0.3805	175	0.3166	2479	X-RAY DIFFRACTION	60
2.6789-2.7276	0.3181	152	0.3225	2650	X-RAY DIFFRACTION	63
2.7276-2.78	0.3361	153	0.3193	2882	X-RAY DIFFRACTION	68
2.78-2.8368	0.3092	153	0.3176	3030	X-RAY DIFFRACTION	72
2.8368-2.8984	0.3143	164	0.3133	3235	X-RAY DIFFRACTION	76
2.8984-2.9658	0.339	177	0.312	3448	X-RAY DIFFRACTION	82
2.9658-3.04	0.3225	180	0.2982	3644	X-RAY DIFFRACTION	86
3.04-3.1221	0.3146	223	0.2903	3848	X-RAY DIFFRACTION	92
3.1221-3.214	0.3047	238	0.2812	4099	X-RAY DIFFRACTION	97
3.214-3.3176	0.3176	215	0.266	4240	X-RAY DIFFRACTION	100
3.3176-3.4362	0.2867	237	0.2592	4193	X-RAY DIFFRACTION	100
3.4362-3.5736	0.2995	213	0.2451	4248	X-RAY DIFFRACTION	100
3.5736-3.7362	0.2749	230	0.2283	4218	X-RAY DIFFRACTION	100
3.7362-3.933	0.2551	240	0.2171	4231	X-RAY DIFFRACTION	100
3.933-4.1791	0.2549	204	0.1934	4265	X-RAY DIFFRACTION	100
4.1791-4.5014	0.2226	231	0.1806	4269	X-RAY DIFFRACTION	100
4.5014-4.9536	0.2263	241	0.1704	4257	X-RAY DIFFRACTION	100
4.9536-5.6686	0.2355	237	0.1987	4292	X-RAY DIFFRACTION	100
5.6686-7.1349	0.2505	208	0.2273	4355	X-RAY DIFFRACTION	100
7.1349-39.3655	0.2048	232	0.1915	4459	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	2.7621	-2.1388	0.7342	4.0829	-1.2334	1.9308	-0.3083	-0.2773	0.7913	0.5272	-0.0455	-0.7246	-0.3521	0.2243	0.3201	0.514	-0.0758	-0.2607	0.5858	-0.1123	0.9521	-4.4862	249.0241	228.8014
2	2.4997	1.4969	0.1307	3.5469	0.2215	2.0478	0.1751	0.2077	-0.348	-0.0731	-0.1759	0.3644	-0.1847	0.0729	0.0546	0.5268	-0.0405	-0.105	0.5049	0.0537	0.8412	-17.7487	271.5417	212.4758
3	1.5238	-0.7249	0.0147	3.8024	-0.0485	1.3049	0.0895	-0.2981	-0.4037	0.3561	-0.0335	-0.2203	0.2171	0.1403	-0.0454	0.4565	-0.0719	-0.1021	0.4701	0.1135	0.5675	0.2218	292.071	223.0973
4	3.0489	0.7623	-0.3036	2.7032	0.5376	2.9192	-0.2636	0.7761	0.5197	-0.4654	0.2201	0.625	-0.4541	-0.0305	0.0226	0.666	-0.1061	-0.1488	0.7289	0.1912	0.8756	15.0429	307.4043	200.9586
5	4.0393	0.8814	0.2097	3.159	0.2434	1.4171	-0.0289	-0.4123	0.6679	0.1208	-0.0691	0.1286	-0.1243	-0.1014	0.0812	0.3988	-0.0664	-0.0641	0.5167	-0.0759	0.6553	32.769	314.4948	223.3438
6	5.4949	-0.7785	0.9038	4.3553	-0.9347	3.3947	-0.231	0.5612	0.9737	-0.1011	-0.1104	-0.4924	-0.0124	0.3823	0.2839	0.3446	-0.0714	0.0219	0.4112	0.1226	0.4628	62.0761	299.8385	223.3646
7	2.6421	-1.266	-0.2948	2.1822	0.7636	2.689	-0.0445	-0.208	-0.1085	0.3856	0.132	-0.0573	0.1128	0.2363	-0.06	0.4917	-0.0418	0.0115	0.3956	-0.0291	0.1862	63.2151	271.3756	227.9741
8	2.086	0.4609	0.0379	3.5134	-0.7497	3.8156	0.1816	0.0852	-0.4698	0.1143	-0.2681	-0.6676	0.2166	-0.0091	0.0768	0.3766	-0.0342	-0.0631	0.3583	-0.1047	0.5427	77.5629	249.4774	212.969
9	3.4908	1.5459	0.1295	5.464	-0.4141	1.9868	-0.0306	-0.3736	-0.3761	0.6239	-0.1953	-0.3558	-0.0061	0.1685	0.162	0.4498	-0.0574	-0.0224	0.4669	-0.0146	0.2935	58.9487	230.5222	224.4577
10	3.0768	0.2622	1.0523	3.8124	-1.5655	4.2157	0.0672	0.1614	-0.166	-0.5401	-0.0146	-0.1879	0.2969	-0.0117	-0.0166	0.3638	-0.0621	0.0488	0.2431	-0.0757	0.18	45.9428	211.8211	203.8683
11	5.3029	1.303	-0.0885	3.1417	-0.8857	0.8273	0.0844	-0.8608	-0.2627	0.438	0.0246	0.5506	-0.1205	-0.1957	-0.0836	0.4319	-0.0641	0.1567	0.5271	0.0688	0.3281	26.4769	206.802	224.9081
12	3.1258	-0.6653	0.4471	2.698	1.1718	2.4232	-0.2183	0.0296	-0.5615	-0.0118	-0.086	0.4425	-0.0083	0.0601	0.2229	0.4437	-0.0064	0.0283	0.4706	0.0558	0.9676	-2.4417	221.2125	222.2287

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 4:322 )
2	X-RAY DIFFRACTION	2	chain A and (resid 323:424 )
3	X-RAY DIFFRACTION	3	chain B and (resid 8:322 )
4	X-RAY DIFFRACTION	4	chain B and (resid 323:421 )
5	X-RAY DIFFRACTION	5	chain C and (resid 9:322 )
6	X-RAY DIFFRACTION	6	chain C and (resid 323:422 )
7	X-RAY DIFFRACTION	7	chain D and (resid 7:322 )
8	X-RAY DIFFRACTION	8	chain D and (resid 323:422 )
9	X-RAY DIFFRACTION	9	chain E and (resid 8:322 )
10	X-RAY DIFFRACTION	10	chain E and (resid 323:422 )
11	X-RAY DIFFRACTION	11	chain F and (resid 10:322 )
12	X-RAY DIFFRACTION	12	chain F and (resid 323:422 )

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