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- PDB-5ykx: The crystal structure of Macrobrachium rosenbergii nodavirus P-do... -

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Basic information

Entry
Database: PDB / ID: 5ykx
TitleThe crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / viral capsid protein
Function / homologyvirion component / Viral coat protein subunit / metal ion binding / : / Capsid protein alpha
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, N.C. / Yoshimura, M. / Lin, C.C. / Guan, H.H. / Chuankhayan, P. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2311-B-213-001-MY3 Taiwan
CitationJournal: Commun Biol / Year: 2019
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi ...Authors: Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen /
Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity ...Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of  = 3 and  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls  = 3 and  = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
History
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4327
Polymers27,7612
Non-polymers6725
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-39 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.175, 134.175, 134.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-201-

CD

21B-201-

CD

31A-334-

HOH

41A-464-

HOH

51B-305-

HOH

61B-414-

HOH

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Components

#1: Protein Capsid protein


Mass: 13880.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XNL3
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.0M Sodium acetate trihydrate, 0.1M Sodium HEPES 7.5, 0.05M Cadmium sulfate 8/3-hydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 28636 / % possible obs: 99.9 % / Redundancy: 20 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.115 / Rsym value: 0.112 / Net I/σ(I): 41.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 19 % / CC1/2: 0.953 / Rpim(I) all: 0.191 / Rrim(I) all: 0.853 / Rsym value: 0.83 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.3 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.354 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19478 1439 5 %RANDOM
Rwork0.15587 ---
obs0.15781 27072 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 23 308 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021938
X-RAY DIFFRACTIONr_bond_other_d0.0010.021799
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9652645
X-RAY DIFFRACTIONr_angle_other_deg0.9934152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4075239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84625.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40815303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.046156
X-RAY DIFFRACTIONr_chiral_restr0.1420.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7622.469962
X-RAY DIFFRACTIONr_mcbond_other2.7512.467961
X-RAY DIFFRACTIONr_mcangle_it3.6983.6791199
X-RAY DIFFRACTIONr_mcangle_other3.73.681200
X-RAY DIFFRACTIONr_scbond_it4.862.926976
X-RAY DIFFRACTIONr_scbond_other4.6322.918972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0074.2111441
X-RAY DIFFRACTIONr_long_range_B_refined24.95926.2312645
X-RAY DIFFRACTIONr_long_range_B_other24.41624.5222454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 102 -
Rwork0.161 1938 -
obs--99.37 %

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