PDB-2wjv: Crystal structure of the complex between human nonsense mediated ...

ID or keywords:

Entry

Database: PDB / ID: 2wjv

Title

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2

Components

REGULATOR OF NONSENSE TRANSCRIPTS 1
REGULATOR OF NONSENSE TRANSCRIPTS 2

Keywords

HYDROLASE / ZINC-FINGER / ATP-BINDING / RNA-BINDING / NONSENSE-MEDIATED MRNA DECAY / NUCLEOTIDE-BINDING / METAL-BINDING

Function / homology

Function and homology information

positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / regulation of telomere maintenance ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Clerici, M. / Mourao, A. / Gutsche, I. / Gehring, N.H. / Hentze, M.W. / Kulozik, A. / Kadlec, J. / Sattler, M. / Cusack, S.

Citation

Journal: Embo J. / Year: 2009
Title: Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, Upf1 and Upf2.
Authors: Clerici, M. / Mourao, A. / Gutsche, I. / Gehring, N.H. / Hentze, M.W. / Kulozik, A. / Kadlec, J. / Sattler, M. / Cusack, S.

History

Deposition	Jun 1, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wjv.cif.gz	338.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wjv.ent.gz	268 KB	Display	PDB format
PDBx/mmJSON format	2wjv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wj/2wjv ftp://data.pdbj.org/pub/pdb/validation_reports/wj/2wjv	HTTPS FTP

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Related structure data

Related structure data	2wjyC 2gk6S 2iykS 1uw4 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6pe8-2 1xcf-1 22357 3m6y-d 2xsa-1 4z31-d 7jjo-d 6oy9-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	#230 - Feb 2019 Initiation Factor eIF4E similarity (5) #245 - May 2020 Spliceosomes similarity (5) #242 - Feb 2020 Coronavirus Proteases similarity (2) #60 - Dec 2004 Ubiquitin similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (2)

Deposited unit

A: REGULATOR OF NONSENSE TRANSCRIPTS 1

B: REGULATOR OF NONSENSE TRANSCRIPTS 1

D: REGULATOR OF NONSENSE TRANSCRIPTS 2

E: REGULATOR OF NONSENSE TRANSCRIPTS 2

hetero molecules

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

1

A: REGULATOR OF NONSENSE TRANSCRIPTS 1

D: REGULATOR OF NONSENSE TRANSCRIPTS 2

hetero molecules

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

2

B: REGULATOR OF NONSENSE TRANSCRIPTS 1

E: REGULATOR OF NONSENSE TRANSCRIPTS 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.410, 97.290, 124.600
Angle α, β, γ (deg.)	90.00, 102.38, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B
1	6	A
2	6	B

NCS domain segments:

Refine code: 1

Dom-ID	Component-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	1	PRO	PRO	PRO	PRO	A	A	119 - 198	5 - 84
2	1	1	PRO	PRO	PRO	PRO	B	B	119 - 198	5 - 84
1	2	1	ASP	ASP	LEU	LEU	A	A	235 - 239	121 - 125
2	2	1	ASP	ASP	LEU	LEU	B	B	235 - 239	121 - 125
1	3	1	PRO	PRO	GLN	GLN	A	A	246 - 256	132 - 142
2	3	1	PRO	PRO	GLN	GLN	B	B	246 - 256	132 - 142
1	4	1	GLN	GLN	ALA	ALA	A	A	261 - 275	147 - 161
2	4	1	GLN	GLN	ALA	ALA	B	B	261 - 275	147 - 161
1	1	2	LEU	LEU	GLN	GLN	A	A	294 - 324	180 - 210
2	1	2	LEU	LEU	GLN	GLN	B	B	294 - 324	180 - 210
1	1	3	LEU	LEU	ASN	ASN	A	A	765 - 905	651 - 791
2	1	3	LEU	LEU	ASN	ASN	B	B	765 - 905	651 - 791
1	1	4	VAL	VAL	GLN	GLN	A	A	414 - 579	300 - 465
2	1	4	VAL	VAL	GLN	GLN	B	B	414 - 579	300 - 465
1	1	5	GLU	GLU	ALA	ALA	A	A	592 - 728	478 - 614
2	1	5	GLU	GLU	ALA	ALA	B	B	592 - 728	478 - 614
1	1	6	GLN	GLN	TRP	TRP	A	A	324 - 333	210 - 219
2	1	6	GLN	GLN	TRP	TRP	B	B	324 - 333	210 - 219
1	2	6	LYS	LYS	LEU	LEU	A	A	340 - 347	226 - 233
2	2	6	LYS	LYS	LEU	LEU	B	B	340 - 347	226 - 233
1	3	6	GLN	GLN	TYR	TYR	A	A	358 - 366	244 - 252
2	3	6	GLN	GLN	TYR	TYR	B	B	358 - 366	244 - 252
1	4	6	PRO	PRO	GLU	GLU	A	A	372 - 394	258 - 280
2	4	6	PRO	PRO	GLU	GLU	B	B	372 - 394	258 - 280
1	5	6	PRO	PRO	VAL	VAL	A	A	402 - 414	288 - 300
2	5	6	PRO	PRO	VAL	VAL	B	B	402 - 414	288 - 300

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (-0.990738, 0.135769, -0.001918), (0.135572, 0.988316, -0.06965), (-0.007561, -0.069265, -0.99757)
Vector: 44.527, -2.8712, 2.3975)

#1: Protein	REGULATOR OF NONSENSE TRANSCRIPTS 1 / UPF1 / ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / UP-FRAMESHIFT SUPPRESSOR 1 ...UPF1 / ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG / NORF1 / HUPF1 Mass: 89984.242 Da / Num. of mol.: 2 / Fragment: CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) References: UniProt: Q92900, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein	REGULATOR OF NONSENSE TRANSCRIPTS 2 / UPF2 / NONSENSE MRNA REDUCING FACTOR 2 / UP-FRAMESHIFT SUPPRESSOR 2 HOMOLOG / HUPF2 Mass: 10640.256 Da / Num. of mol.: 2 / Fragment: C-TERMINAL REGION, RESIDUES 1105-1198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR(DE3) / References: UniProt: Q9HAU5
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO₄
Nonpolymer details	SUPHATE ION (SO4): FROM CRYSTALLISATION MEDIUM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.7 % / Description: NONE
Crystal grow	pH: 6.5 Details: 1.5-1.6M AMMONIUM SULPHATE, 100 MM MES PH 6.3-6.5 AND 2% V/V GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 23, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.94 Å / Relative weight: 1
Reflection	Resolution: 2.85→30 Å / Num. obs: 49227 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 3.88 % / R_merge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0038	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2GK6 AND 2IYK

2gk6

2iyk

Resolution: 2.85→48.79 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.917 / SU B: 32.993 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	2463	5 %	RANDOM
R_work	0.2	-	-	-
obs	0.203	46534	96.9 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.98 Å²	0 Å²	0.41 Å²
2-	-	0.5 Å²	0 Å²
3-	-	-	-1.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→48.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13066	0	121	0	13187

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	13409
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9159
X-RAY DIFFRACTION	r_angle_refined_deg	1.228	1.974	18147
X-RAY DIFFRACTION	r_angle_other_deg	0.839	3	22417
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.977	5	1636
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.567	24.61	603
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.519	15	2403
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.182	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	2028
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	14593
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2527
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	0.458	1.5	8240
X-RAY DIFFRACTION	r_mcbond_other	0.062	1.5	3316
X-RAY DIFFRACTION	r_mcangle_it	0.89	2	13322
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.204	3	5169
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.07	4.5	4825
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1497	tight positional	0.02	0.05
1	2	B	1497	tight positional	0.02	0.05
2	1	A	458	tight positional	0.02	0.05
2	2	B	458	tight positional	0.02	0.05
3	1	A	1918	tight positional	0.02	0.05
3	2	B	1918	tight positional	0.02	0.05
4	1	A	2175	tight positional	0.03	0.05
4	2	B	2175	tight positional	0.03	0.05
5	1	A	1797	tight positional	0.03	0.05
5	2	B	1797	tight positional	0.03	0.05
6	1	A	828	tight positional	0.02	0.05
6	2	B	828	tight positional	0.02	0.05
1	1	A	1497	tight thermal	0.93	10
1	2	B	1497	tight thermal	0.93	10
2	1	A	458	tight thermal	1.15	10
2	2	B	458	tight thermal	1.15	10
3	1	A	1918	tight thermal	1.11	10
3	2	B	1918	tight thermal	1.11	10
4	1	A	2175	tight thermal	1.29	10
4	2	B	2175	tight thermal	1.29	10
5	1	A	1797	tight thermal	1.27	10
5	2	B	1797	tight thermal	1.27	10
6	1	A	828	tight thermal	1.21	10
6	2	B	828	tight thermal	1.21	10

LS refinement shell

Resolution: 2.85→2.92 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	182	-
R_work	0.332	3418	-
obs	-	-	96.98 %

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	5.1142	1.3321	1.9696	3.0685	-0.625	4.7723	-0.0128	0.3091	0.1565	-0.1014	0.0603	-0.3501	0.1879	0.5103	-0.0474	0.3761	0.1303	-0.0478	0.7288	-0.1104	0.3501	77.707	-0.445	59.482
2	5.3865	-1.4804	2.482	3.7046	0.0356	5.5255	-0.0318	-0.3428	0.3845	0.1555	-0.0091	0.3461	0.1054	-0.6778	0.0409	0.3083	-0.1293	-0.0155	0.6304	-0.0029	0.3004	-33.997	3.578	-57.486
3	2.2818	-0.1233	-0.2199	3.0001	-0.1396	3.2965	0.118	0.2099	0.237	-0.157	0.012	-0.1708	-0.1594	0.4428	-0.1299	0.2233	-0.1608	-0.0989	0.4729	0.0012	0.1587	46.187	4.019	30.207
4	7.6685	-0.3332	-1.4105	6.8144	3.8396	13.7801	0.3356	0.8024	-0.0364	-0.8776	-0.381	-0.3765	-0.7075	0.3407	0.0455	1.0841	0.0351	-0.2059	0.7749	-0.1169	0.4512	43.389	-15.89	3.97
5	3.3198	1.743	0.5404	8.8788	2.5819	5.3235	-0.146	-0.0664	0.0382	0.0236	-0.0355	0.9334	0.338	-0.3713	0.1815	0.1137	-0.139	-0.0438	0.5103	0.0681	0.3754	13.552	-9.381	28
6	2.2349	0.0168	-0.1779	2.6548	0.489	2.6069	0.1511	-0.1527	0.1433	0.0871	-0.0097	-0.1081	0.0354	-0.2019	-0.1415	0.1981	0.0863	-0.1434	0.3955	-0.0047	0.1563	-0.876	5.175	-28.069
7	6.6399	0.7366	-0.0705	14.7509	-10.0367	18.8512	0.0735	-0.5287	0.0854	1.6298	0.1299	0.7048	-1.8706	-0.8568	-0.2034	1.0251	0.1402	-0.1355	0.5588	0.093	0.4411	-0.637	-12.556	-0.782
8	4.3765	-2.1194	0.0942	8.7608	-2.7145	4.7589	-0.3571	-0.3618	-0.0367	0.3712	0.1874	-0.6612	0.4555	0.317	0.1697	0.2163	0.2436	-0.1297	0.5817	-0.1135	0.3355	30.07	-12.411	-25.43

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 3
2	X-RAY DIFFRACTION	1	A	116 - 280
3	X-RAY DIFFRACTION	1	D	1102 - 1198
4	X-RAY DIFFRACTION	2	B	1 - 3
5	X-RAY DIFFRACTION	2	B	116 - 280
6	X-RAY DIFFRACTION	2	E	1102 - 1198
7	X-RAY DIFFRACTION	3	A	286 - 323
8	X-RAY DIFFRACTION	3	A	415 - 699
9	X-RAY DIFFRACTION	4	A	324 - 414
10	X-RAY DIFFRACTION	5	A	700 - 911
11	X-RAY DIFFRACTION	6	B	288 - 323
12	X-RAY DIFFRACTION	6	B	415 - 699
13	X-RAY DIFFRACTION	7	B	324 - 414
14	X-RAY DIFFRACTION	8	B	700 - 913

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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

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Yorodumi