[English] 日本語
Yorodumi
- PDB-3pa2: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pa2
TitleCrystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type Ley
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA)
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lewis Y antigen, beta anomer / IMIDAZOLE / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHansman, G.S. / Biertumpfel, C. / Chen, L. / Georgiev, I. / McLellan, J.S. / Katayama, K. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability.
Authors: Hansman, G.S. / Biertumpfel, C. / Georgiev, I. / McLellan, J.S. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,72026
Polymers69,6102
Non-polymers2,11024
Water13,781765
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,48118
Polymers34,8051
Non-polymers1,67617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2398
Polymers34,8051
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.271, 79.130, 69.069
Angle α, β, γ (deg.)90.00, 100.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Capsid protein


Mass: 34804.953 Da / Num. of mol.: 2 / Fragment: P-domain-026 (UNP residues 224 to 538)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: Vietnam 026 / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F4T5
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis Y antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Imidazol, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→29.08 Å / Num. all: 114707 / Num. obs: 114707 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.057 / Net I/σ(I): 16.3
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.647 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASER(2.1.4)phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ONU

3onu


Resolution: 1.48→29.08 Å / SU ML: 0.17 / Isotropic thermal model: Isotropic, TLS / σ(F): 0 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 5772 5.03 %
Rwork0.1848 --
obs0.1857 114698 99.78 %
all-114698 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.241 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.351 Å20 Å2-2.9715 Å2
2---1.1312 Å2-0 Å2
3---1.4822 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 139 765 5727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075137
X-RAY DIFFRACTIONf_angle_d1.126998
X-RAY DIFFRACTIONf_dihedral_angle_d14.7991861
X-RAY DIFFRACTIONf_chiral_restr0.075785
X-RAY DIFFRACTIONf_plane_restr0.006915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.49680.2962030.28923590X-RAY DIFFRACTION100
1.4968-1.51440.28952020.27963605X-RAY DIFFRACTION100
1.5144-1.53290.3261940.26843608X-RAY DIFFRACTION100
1.5329-1.55230.25271860.25323652X-RAY DIFFRACTION100
1.5523-1.57270.25031910.24523579X-RAY DIFFRACTION100
1.5727-1.59430.27611740.23233652X-RAY DIFFRACTION100
1.5943-1.6170.27332120.23473573X-RAY DIFFRACTION100
1.617-1.64120.24861910.22313664X-RAY DIFFRACTION100
1.6412-1.66680.23692110.21613585X-RAY DIFFRACTION100
1.6668-1.69410.24711920.20343645X-RAY DIFFRACTION100
1.6941-1.72340.20151880.20123631X-RAY DIFFRACTION100
1.7234-1.75470.21881670.18973625X-RAY DIFFRACTION100
1.7547-1.78840.20812000.18143613X-RAY DIFFRACTION100
1.7884-1.82490.20731940.18243616X-RAY DIFFRACTION100
1.8249-1.86460.20151980.17813662X-RAY DIFFRACTION100
1.8646-1.9080.23011900.17793598X-RAY DIFFRACTION100
1.908-1.95570.18652100.17653603X-RAY DIFFRACTION100
1.9557-2.00850.19361970.17593648X-RAY DIFFRACTION100
2.0085-2.06760.19971770.17873634X-RAY DIFFRACTION100
2.0676-2.13430.23111780.17913665X-RAY DIFFRACTION100
2.1343-2.21060.18341940.1763612X-RAY DIFFRACTION100
2.2106-2.29910.18782080.17473620X-RAY DIFFRACTION100
2.2991-2.40370.1982140.17363617X-RAY DIFFRACTION100
2.4037-2.53030.19461910.17733621X-RAY DIFFRACTION100
2.5303-2.68880.20241800.18393652X-RAY DIFFRACTION100
2.6888-2.89620.20561950.18293642X-RAY DIFFRACTION100
2.8962-3.18730.19241720.17553668X-RAY DIFFRACTION100
3.1873-3.64780.19381890.17233675X-RAY DIFFRACTION100
3.6478-4.59290.16412060.1543628X-RAY DIFFRACTION99
4.5929-29.08550.1861680.18363743X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.51210.0498-0.11840.543-0.11330.4163-0.01850.07840.0015-0.02010.0361-0.0062-0.08490.0103-0.02380.0459-0.00680.00970.0493-0.00090.01468.08666.41998.675
20.53230.12640.2260.61390.07290.47470.05850.0384-0.13170.06140.0292-0.17040.03980.0767-0.08140.04970.006-0.02880.0572-0.00980.109620.6283-6.030324.5788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more