PDB-2yhm: Structure of respiratory syncytial virus nucleocapsid protein, P2...

ID or keywords:

Entry

Database: PDB / ID: 2yhm

Title

Structure of respiratory syncytial virus nucleocapsid protein, P212121 crystal form

Components

NUCLEOPROTEIN
RNA

Keywords

VIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA COMPLEX

Function / homology

Function and homology information

Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / Respiratory syncytial virus genome replication / helical viral capsid / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...
Similarity search - Function

Biological species

HUMAN RESPIRATORY SYNCYTIAL VIRUS

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.6 Å

Authors

El Omari, K. / Dhaliwal, B. / Ren, J. / Abrescia, N.G.A. / Lockyer, M. / Powell, K.L. / Hawkins, A.R. / Stammers, D.K.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of Respiratory Syncytial Virus Nucleocapsid Protein from Two Crystal Forms: Details of Potential Packing Interactions in the Native Helical Form.
Authors: El Omari, K. / Dhaliwal, B. / Ren, J. / Abrescia, N.G.A. / Lockyer, M. / Powell, K.L. / Hawkins, A.R. / Stammers, D.K.

History

Deposition	May 4, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim 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 / _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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Download

PDBx/mmCIF format	2yhm.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb2yhm.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	2yhm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2yhm_validation.pdf.gz	537.2 KB	Display	wwPDB validaton report
Full document	2yhm_full_validation.pdf.gz	618.1 KB	Display
Data in XML	2yhm_validation.xml.gz	127.6 KB	Display
Data in CIF	2yhm_validation.cif.gz	172.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/2yhm ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yhm	HTTPS FTP

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Related structure data

Related structure data	4v5vC 2wj8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4v5v-2 4v5v-3 4v5v-1 4v5v-4 2wj8-1 2wj8-2 5fvc-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: NUCLEOPROTEIN

B: NUCLEOPROTEIN

C: NUCLEOPROTEIN

D: NUCLEOPROTEIN

E: NUCLEOPROTEIN

F: NUCLEOPROTEIN

G: NUCLEOPROTEIN

H: NUCLEOPROTEIN

I: NUCLEOPROTEIN

J: NUCLEOPROTEIN

K: RNA

438 kDa, 11 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)	133.607, 149.914, 255.196
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 375 / Label seq-ID: 1 - 375

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J

#1: Protein	NUCLEOPROTEIN / RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N Mass: 41659.820 Da / Num. of mol.: 10 / Fragment: RESIDUES 1-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03418
#2: RNA chain	RNA Mass: 21317.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
Sequence details	NON SPECIFIC RNA FROM CELLULAR ORIGIN BOUND TO THE NUCLEOPROTEIN

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60 % / Description: NONE
Crystal grow	pH: 7 Details: 10% (W/V) PEG 400, 0.1 M KCL, 0.05 M HEPES PH 7.0, 0.01 M CACL2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 3.6→30 Å / Num. obs: 53027 / % possible obs: 81.7 % / Observed criterion σ(I): 2.5 / Redundancy: 11.2 % / R_merge(I) obs: 0.14 / Net I/σ(I): 14.1
Reflection shell	Resolution: 3.6→3.73 Å / Redundancy: 10.9 % / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 2.5 / % possible all: 66.2

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0077	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ8

2wj8

Resolution: 3.6→50 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.927 / SU B: 72.231 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.698 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22359	2560	5.1 %	RANDOM
R_work	0.19634	-	-	-
obs	0.19778	47566	83.41 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 102.754 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.95 Å²	0 Å²	0 Å²
2-	-	-4.53 Å²	0 Å²
3-	-	-	-2.42 Å²

Refinement step

Cycle: LAST / Resolution: 3.6→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29200	1400	0	0	30600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	31219
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.091	1.941	42356
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.56	5	3740
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.441	24.504	1310
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.419	15	5470
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.841	15	160
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	4790
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	22590
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Ens-ID: 1 / Number: 2920 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.02	0.05
2	B	tight positional	0.02	0.05
3	C	tight positional	0.02	0.05
4	D	tight positional	0.02	0.05
5	E	tight positional	0.02	0.05
6	F	tight positional	0.02	0.05
7	G	tight positional	0.02	0.05
8	H	tight positional	0.02	0.05
9	I	tight positional	0.02	0.05
10	J	tight positional	0.02	0.05
1	A	tight thermal	10.58	0.5
2	B	tight thermal	8.08	0.5
3	C	tight thermal	7.81	0.5
4	D	tight thermal	7.24	0.5
5	E	tight thermal	10.43	0.5
6	F	tight thermal	8.37	0.5
7	G	tight thermal	6.77	0.5
8	H	tight thermal	8.55	0.5
9	I	tight thermal	8.76	0.5
10	J	tight thermal	8.95	0.5

LS refinement shell

Resolution: 3.6→3.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	154	-
R_work	0.277	2762	-
obs	-	-	66.76 %

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	2.3472	-0.0676	-0.9997	2.1059	-0.1315	3.3567	-0.1221	0.2264	-0.1835	0.0377	0.051	-0.0093	0.2228	-0.165	0.0711	0.2936	0.0837	-0.1938	0.3834	-0.0939	0.3141	4.673	-11.5747	-30.4334
2	0.0847	0.0022	0.0097	0.0708	0.0028	0.0061	0.0078	0.0866	-0.0201	0.0293	-0.0127	0.1251	0.0057	-0.0187	0.0049	0.5103	0.0621	0.0073	0.2688	-0.066	0.2324	-8.9533	30.3183	0.0282
3	3.1855	0.7847	-1.0072	3.2327	-0.7703	2.8324	-0.1544	0.3168	-0.1936	-0.549	0.2295	-0.1252	0.1038	0.0296	-0.0751	0.4179	0.1289	-0.1924	0.3848	-0.232	0.323	2.3505	14.5432	-49.4169
4	3.5888	1.3961	-0.0889	3.9364	-0.6418	1.9058	-0.0451	0.4095	-0.0584	-0.4614	0.1119	0.0027	-0.0597	0.2287	-0.0668	0.4014	0.1525	-0.1449	0.4389	-0.1983	0.111	-0.0364	46.6021	-49.4876
5	3.4143	1.701	0.6374	3.6182	0.6822	1.4759	-0.0897	0.1938	0.2592	-0.4333	0.126	0.1144	-0.3074	0.1832	-0.0363	0.4835	0.1634	-0.1108	0.3732	-0.0221	0.0684	-1.4939	72.8028	-31.0408
6	3.0892	0.5089	1.0198	2.5585	1.0854	3.0889	0.0086	0.1263	0.2646	-0.2571	-0.1073	0.1471	-0.4351	-0.1522	0.0987	0.4417	0.1657	0.0224	0.0983	0.0238	0.104	-1.9454	82.9801	-0.5385
7	2.9134	0.0636	1.1603	1.8043	0.2098	3.8608	-0.0348	-0.0853	0.1084	-0.0795	-0.0893	0.0896	-0.3046	-0.1791	0.1241	0.3169	0.086	0.1381	0.0346	0.0027	0.1832	-1.578	73.504	29.9384
8	3.98	-0.71	1.17	2.7105	-1.1222	2.8735	-0.1016	-0.4063	0.0685	0.2537	0.0933	0.049	-0.168	-0.1258	0.0082	0.3108	-0.0055	0.2195	0.0773	-0.0757	0.2559	0.0204	47.8794	49.5135
9	4.3474	-1.1769	0.5853	3.4113	-0.9406	2.2888	-0.0503	-0.312	-0.287	0.0908	0.0256	-0.0391	0.0204	0.0319	0.0247	0.347	-0.08	0.2086	0.0613	-0.0382	0.1577	2.9092	15.8222	49.7561
10	3.6915	-1.7491	-1.118	3.6935	0.5947	1.9076	0.0291	-0.057	-0.163	0.1956	-0.0635	0.0014	0.1263	0.0517	0.0344	0.4439	-0.1069	0.0161	0.0952	-0.0763	0.0982	5.7355	-10.1793	30.9934
11	5.926	-0.9105	-1.9303	2.3939	0.5238	2.6016	-0.0731	0.6576	-0.4532	0.121	-0.2655	0.0634	0.0245	-0.1321	0.3386	0.3142	0.0012	-0.0567	0.2189	-0.0911	0.216	6.2676	-20.8542	0.5998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 375
2	X-RAY DIFFRACTION	2	K	1 - 70
3	X-RAY DIFFRACTION	3	B	1 - 375
4	X-RAY DIFFRACTION	4	C	1 - 375
5	X-RAY DIFFRACTION	5	D	1 - 375
6	X-RAY DIFFRACTION	6	E	1 - 375
7	X-RAY DIFFRACTION	7	F	1 - 375
8	X-RAY DIFFRACTION	8	G	1 - 375
9	X-RAY DIFFRACTION	9	H	1 - 375
10	X-RAY DIFFRACTION	10	I	1 - 375
11	X-RAY DIFFRACTION	11	J	1 - 375

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

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Jul 12, 2017. Major update of PDB

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Yorodumi