PDB-3ow8: Crystal Structure of the WD repeat-containing protein 61

ID or keywords:

Entry

Database: PDB / ID: 3ow8

Title

Crystal Structure of the WD repeat-containing protein 61

Components

WD repeat-containing protein 61

Keywords

TRANSCRIPTION / WD repeat / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

Ski complex / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / negative regulation of myeloid cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / transcription elongation by RNA polymerase II ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Tempel, W. / Li, Z. / Chao, X. / Lam, R. / Wernimont, A.K. / He, H. / Seitova, A. / Pan, P.W. / Li, Y. / Bountra, C. ...

Citation

Journal: Protein Cell / Year: 2011
Title: Structure and function of WD40 domain proteins.
Authors: Xu, C. / Min, J.

History

Deposition	Sep 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 29, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif 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 / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ow8.cif.gz	443.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ow8.ent.gz	363.2 KB	Display	PDB format
PDBx/mmJSON format	3ow8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ow8_validation.pdf.gz	457.5 KB	Display	wwPDB validaton report
Full document	3ow8_full_validation.pdf.gz	463.8 KB	Display
Data in XML	3ow8_validation.xml.gz	38.9 KB	Display
Data in CIF	3ow8_validation.cif.gz	54.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/3ow8 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3ow8	HTTPS FTP

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Related structure data

Related structure data	3e0cC 3fm0C 3gfcC 3i2nC 3frxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vfc-d 2h9m-2 2o9k-2 4o45-d 2o9k-1 5sxm-1 4qqe-d 2h9m-1 2co0-1 2h13-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) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#86 - Feb 2007 Exosomes similarity (1) #145 - Jan 2012 Messenger RNA Capping similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (3) #67 - Jul 2005 TATA-Binding Protein similarity (1)

Deposited unit

A: WD repeat-containing protein 61

B: WD repeat-containing protein 61

C: WD repeat-containing protein 61

D: WD repeat-containing protein 61

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

1

A: WD repeat-containing protein 61

defined by software
35.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: WD repeat-containing protein 61

defined by software
35.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: WD repeat-containing protein 61

defined by software
35.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: WD repeat-containing protein 61

defined by software
35.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.544, 72.922, 81.514
Angle α, β, γ (deg.)	114.340, 96.440, 90.120
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	C
2	2	D
1	3	A
2	3	C
1	4	A
2	4	C
1	5	B
2	5	C
1	6	B
2	6	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	TYR	TYR	LEU	LEU	2	A	A	5 - 60	21 - 76
2	1	1	TYR	TYR	LEU	LEU	2	B	B	5 - 60	21 - 76
1	2	1	GLN	GLN	LEU	LEU	4	A	A	64 - 228	80 - 244
2	2	1	GLN	GLN	LEU	LEU	4	B	B	64 - 228	80 - 244
1	3	1	ALA	ALA	PRO	PRO	4	A	A	232 - 304	248 - 320
2	3	1	ALA	ALA	PRO	PRO	4	B	B	232 - 304	248 - 320
1	1	2	TYR	TYR	PRO	PRO	2	C	C	5 - 304	21 - 320
2	1	2	TYR	TYR	PRO	PRO	2	D	D	5 - 304	21 - 320
1	1	3	SER	SER	HIS	HIS	2	A	A	229 - 231	245 - 247
2	1	3	SER	SER	HIS	HIS	2	C	C	229 - 231	245 - 247
1	1	4	GLU	GLU	HIS	HIS	2	A	A	61 - 63	77 - 79
2	1	4	GLU	GLU	HIS	HIS	2	C	C	61 - 63	77 - 79
1	1	5	SER	SER	HIS	HIS	3	B	B	229 - 231	245 - 247
2	1	5	SER	SER	HIS	HIS	3	C	C	229 - 231	245 - 247
1	1	6	GLU	GLU	HIS	HIS	3	B	B	61 - 63	77 - 79
2	1	6	GLU	GLU	HIS	HIS	3	C	C	61 - 63	77 - 79

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog Mass: 35629.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9GZS3
#2: Chemical	... ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 35 / Source method: obtained synthetically

#1: Protein

WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog

Mass: 35629.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: WDR61 / Plasmid: pFBOH-MHL / Production host:

Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9GZS3

#2: Chemical

...
ChemComp-UNX / UNKNOWN ATOM OR ION

Num. of mol.: 35 / Source method: obtained synthetically

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.46 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, ...Details: Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, sitting drop, temperature 291K

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.46 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop
Details: Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97934 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.3→40 Å / Num. obs: 58481 / % possible obs: 97.8 % / Redundancy: 1.9 % / R_merge(I) obs: 0.106 / Χ²: 1.868 / Net I/σ(I): 9.89

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.3-2.34	1.8	0.865	1.05	2898	1.915	96
2.34-2.38	1.8	0.781		2882	1.783	96.8
2.38-2.43	1.8	0.735		2905	1.812	96.9
2.43-2.48	1.9	0.635		2894	1.688	97.3
2.48-2.53	1.9	0.582		2913	1.902	97.4
2.53-2.59	1.9	0.564		2931	1.826	97.5
2.59-2.66	1.9	0.444		2902	1.809	97.5
2.66-2.73	1.9	0.374		2918	1.905	97.6
2.73-2.81	1.9	0.324		2970	1.899	98.1
2.81-2.9	1.9	0.265		2886	1.939	98
2.9-3	1.9	0.198		2923	1.784	98.2
3-3.12	1.9	0.174		2963	1.93	98.2
3.12-3.26	1.9	0.132		2929	1.87	98.2
3.26-3.44	1.9	0.104		2918	1.893	98.2
3.44-3.65	1.9	0.079		2950	1.89	98.5
3.65-3.93	1.9	0.068		2936	1.943	98.3
3.93-4.33	1.9	0.055		2952	1.943	98.5
4.33-4.95	1.9	0.042		2947	1.818	98.5
4.95-6.24	1.9	0.048		2937	1.727	98.9
6.24-40	2	0.046		2927	2.057	97.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3frx

3frx

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.894 / WR_factor R_free: 0.257 / WR_factor R_work: 0.226 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.543 / SU ML: 0.245
Cross valid method: THROUGHOUT. Change of flag assignment was followed by slow-cool simulated annealing (from temperature = 5000.0, phenix).
σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Programs chainsaw, resolve, buccaneer, phenix, autobuster, coot and the molprobity server were also used during refinement.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2766	2000	3.434 %	phenix.reflection_file_converter --use-lattice-symmetry-in-r-free-flag-generation
R_work	0.244	-	-	-
obs	0.245	58241	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso max: 79.65 Å² / B_iso mean: 29.377 Å² / B_iso min: 19.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.228 Å²	-0.256 Å²	-0.235 Å²
2-	-	-0.925 Å²	0.491 Å²
3-	-	-	3.505 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8828	0	35	0	8863

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	9056
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5573
X-RAY DIFFRACTION	r_angle_refined_deg	1.1	1.919	12391
X-RAY DIFFRACTION	r_angle_other_deg	0.812	3	13657
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.18	5	1179
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.43	24.768	367
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.38	15	1266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.022	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1413
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10364
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1843
X-RAY DIFFRACTION	r_mcbond_it	0.249	1.5	5852
X-RAY DIFFRACTION	r_mcbond_other	0.066	1.5	2433
X-RAY DIFFRACTION	r_mcangle_it	0.456	2	9326
X-RAY DIFFRACTION	r_scbond_it	0.79	3	3204
X-RAY DIFFRACTION	r_scangle_it	1.213	4.5	3065

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	285	TIGHT POSITIONAL	0.07	0.05
1	A	3128	MEDIUM POSITIONAL	0.11	0.5
1	A	285	TIGHT THERMAL	0.19	0.5
1	A	3128	MEDIUM THERMAL	0.19	2
2	C	1766	TIGHT POSITIONAL	0.02	0.05
2	C	1875	MEDIUM POSITIONAL	0.02	0.5
2	C	1766	TIGHT THERMAL	0.04	0.5
2	C	1875	MEDIUM THERMAL	0.04	2
3	A	17	TIGHT POSITIONAL	0.04	0.05
3	A	13	MEDIUM POSITIONAL	0.03	0.5
3	A	17	TIGHT THERMAL	0.04	0.5
3	A	13	MEDIUM THERMAL	0.05	2
4	A	17	TIGHT POSITIONAL	0.02	0.05
4	A	21	MEDIUM POSITIONAL	0.03	0.5
4	A	17	TIGHT THERMAL	0.05	0.5
4	A	21	MEDIUM THERMAL	0.05	2
5	B	17	TIGHT POSITIONAL	0.03	0.05
5	B	13	LOOSE POSITIONAL	0.03	5
5	B	17	TIGHT THERMAL	0.05	0.5
5	B	13	LOOSE THERMAL	0.09	10
6	B	17	TIGHT POSITIONAL	0.01	0.05
6	B	21	LOOSE POSITIONAL	0.04	5
6	B	17	TIGHT THERMAL	0.06	0.5
6	B	21	LOOSE THERMAL	0.05	10

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.3-2.359	0.402	148	0.378	4025	4173
2.359-2.424	0.422	147	0.371	3987	4134
2.424-2.493	0.34	136	0.353	3952	4088
2.493-2.57	0.405	132	0.336	3756	3888
2.57-2.653	0.353	133	0.315	3689	3822
2.653-2.746	0.31	123	0.29	3553	3676
2.746-2.848	0.301	119	0.263	3450	3569
2.848-2.963	0.34	118	0.253	3357	3475
2.963-3.094	0.283	112	0.237	3208	3320
3.094-3.243	0.279	117	0.229	3064	3181
3.243-3.416	0.249	97	0.227	2903	3000
3.416-3.621	0.243	96	0.219	2797	2893
3.621-3.867	0.249	93	0.221	2578	2671
3.867-4.171	0.217	88	0.2	2421	2509
4.171-4.56	0.201	80	0.177	2247	2327
4.56-5.084	0.2	77	0.18	2019	2096
5.084-5.842	0.252	61	0.229	1820	1881
5.842-7.088	0.334	56	0.254	1526	1582
7.088-9.756	0.253	43	0.262	1197	1240
9.756-30	0.289	24	0.26	692	716

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	2.5128	0.4818	0.1022	2.6918	-0.0018	2.1441	0.0844	-0.2337	0.3174	0.3174	-0.1291	0.308	-0.214	-0.0735	0.0447	0.1398	-0.0036	0.0257	0.0281	-0.0474	0.13	11.7708	20.2199	51.7681
2	2.2668	-0.0707	-0.0318	2.3743	0.2722	1.8823	0.058	0.1592	-0.2039	-0.1631	-0.0313	0.0732	0.1909	-0.0664	-0.0268	0.123	0.0149	-0.0413	0.0236	-0.0046	0.058	-20.6897	26.6757	19.7435
3	2.5936	0.2829	0.3055	1.7898	0.451	2.0754	-0.0249	0.2357	0.2493	-0.2767	-0.0405	0.0661	-0.1602	-0.0054	0.0654	0.0518	0.0081	-0.0155	0.025	0.0239	0.0376	-19.353	-12.5286	19.7952
4	2.3019	-0.0903	0.1264	2.1488	0.3048	1.9569	0.0468	-0.2058	-0.1123	0.2779	-0.0632	0.0602	0.1563	-0.1114	0.0164	0.0486	-0.0173	0.0042	0.0255	0.0069	0.0077	13.0173	-13.3138	51.8319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999

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Yorodumi