[English] 日本語
Yorodumi
- PDB-4pn6: Structure of the Cytomegalovirus-Encoded m04 Glycoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pn6
TitleStructure of the Cytomegalovirus-Encoded m04 Glycoprotein
ComponentsM04
KeywordsVIRAL PROTEIN
Function / homologyImmunoglobulin-like - #2900 / Gp34-like superfamily / Immune evasion protein / Immune evasion protein / membrane => GO:0016020 / Immunoglobulin-like / Sandwich / Mainly Beta / M04
Function and homology information
Biological speciesMuromegalovirus G4
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsBerry, R. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Structure of the Cytomegalovirus-Encoded m04 Glycoprotein, a Prototypical Member of the m02 Family of Immunoevasins.
Authors: Berry, R. / Vivian, J.P. / Deuss, F.A. / Balaji, G.R. / Saunders, P.M. / Lin, J. / Littler, D.R. / Brooks, A.G. / Rossjohn, J.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / diffrn_source / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_oper_list / refine_hist / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_asym.entity_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0 : statistics at the very beginning when nothing is done yet

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M04
B: M04
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6988
Polymers48,0302
Non-polymers2,6676
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint17 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.040, 94.040, 122.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein M04


Mass: 24015.234 Da / Num. of mol.: 2 / Fragment: UNP residues 24-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muromegalovirus G4 / Gene: m04 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: B3UWV7
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 23% Peg3350, 0.2M Sodium Acetate ph4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 3→74.6 Å / Num. obs: 11576 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 85.85 Å2 / Net I/σ(I): 9.7

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 3→66.5 Å / Cor.coef. Fo:Fc: 0.9043 / Cor.coef. Fo:Fc free: 0.8864 / SU R Cruickshank DPI: 1.799 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 5.328 / SU Rfree Blow DPI: 0.357 / SU Rfree Cruickshank DPI: 0.358
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 554 4.8 %RANDOM
Rwork0.2213 ---
obs0.2224 11534 99.78 %-
Displacement parametersBiso mean: 92.22 Å2
Baniso -1Baniso -2Baniso -3
1--5.2386 Å20 Å20 Å2
2---5.2386 Å20 Å2
3---10.4772 Å2
Refine analyzeLuzzati coordinate error obs: 0.515 Å
Refinement stepCycle: 1 / Resolution: 3→66.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 176 0 2789
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072872HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963937HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes408HARMONIC5
X-RAY DIFFRACTIONt_it2872HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.94
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2896SEMIHARMONIC4
LS refinement shellResolution: 3→3.29 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2611 126 4.66 %
Rwork0.2448 2577 -
all0.2456 2703 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 26.1731 Å / Origin y: 18.9175 Å / Origin z: 50.3428 Å
111213212223313233
T-0.2407 Å2-0.1635 Å2-0.0247 Å2--0.1343 Å20.0016 Å2---0.2737 Å2
L1.2816 °2-0.4548 °2-0.3986 °2-2.8272 °2-0.7046 °2--2.7849 °2
S0.0425 Å °0.216 Å °0.1614 Å °-0.4981 Å °0.1526 Å °-0.2015 Å °-0.0848 Å °0.3746 Å °-0.1951 Å °
Refinement TLS groupSelection details: { *|* }

+
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://pdbjlvh1.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