[English] 日本語
Yorodumi
- PDB-4jm0: Structure of Human Cytomegalovirus Immune Modulator UL141 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jm0
TitleStructure of Human Cytomegalovirus Immune Modulator UL141
ComponentsProtein UL141
KeywordsCELL ADHESION / viral protein in complex with human receptor / Immunoglobulin-like V-set folg of N-terminal domain / Ig-like beta sandwich domain / viral immunomodulator / host-virus interaction / TRAIL-R2 / CD155 / glycosylation / membrane
Function / homology
Function and homology information


evasion by virus of host natural killer cell activity / host cell endoplasmic reticulum membrane / membrane
Similarity search - Function
Immunoglobulin-like - #3790 / Herpesvirus membrane glycoprotein UL141 / UL141-like superfamily / Herpes-like virus membrane glycoprotein UL141 / Immunoglobulin-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsNemcovicova, I. / Zajonc, D.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding.
Authors: Nemcovicova, I. / Zajonc, D.M.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Oct 19, 2016Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein UL141
B: Protein UL141
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9617
Polymers58,8392
Non-polymers2,1225
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-27 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.060, 96.060, 136.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9725, 0.232284, -0.01695), (0.232301, 0.972643, 0.00103), (0.016726, -0.002936, -0.999856)-18.33501, 2.12478, 40.82166

-
Components

#1: Protein Protein UL141


Mass: 29419.320 Da / Num. of mol.: 2 / Fragment: UL141 ECTODOMAIN, UNP residues 30-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Strain: Merlin / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6RJQ3
#2: 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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 295.15 K / pH: 8
Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8, 10% (w/v) polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.25→11.98 Å / Num. obs: 10665 / % possible obs: 75 % / Observed criterion σ(I): 2
Reflection shellResolution: 3.25→3.33 Å / % possible all: 97

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0104refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→11.98 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.849 / SU B: 41.504 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.279 930 8 %RANDOM
Rwork0.201 ---
obs0.201 10665 97.5 %-
all-20356 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 3.25→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 140 0 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3521.9884038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2835350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12722.92113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.0491515
X-RAY DIFFRACTIONr_chiral_restr0.1270.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212193
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 59 -
Rwork0.253 674 -
obs--99.46 %
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)
11.85560.29551.55621.75210.26015.81450.30590.244-0.5696-0.1313-0.1547-0.03410.99180.2269-0.15130.2331-0.022-0.00470.5073-0.03080.3027-1.663834.849912.6762
211.7571-1.927411.45121.7148-6.763729.31960.91281.0609-0.7729-0.37560.1360.15811.12430.4749-1.04880.4198-0.09440.09310.4726-0.05510.14857.404536.1328.3823
34.3479-0.59341.30492.5125-0.55255.04410.03680.2423-0.3043-0.1586-0.0425-0.12990.1665-0.18430.00570.0420.00740.05350.2725-0.01920.10192.693339.914610.443
48.1992-2.6675-1.3235.8663-1.609823.37370.38640.5738-0.3272-1.08890.07030.05720.1412-0.7368-0.45670.2846-0.1258-0.0950.4807-0.09680.3035-15.402437.3477-2.4413
52.4094-6.0917-3.247315.46618.25744.41530.41130.4353-0.5424-0.8756-0.96571.0943-0.41-0.55610.55440.89510.0088-0.28820.8252-0.18711.5088-7.042226.581-0.0743
622.0057-12.2938-6.330112.8633-0.74114.8967-0.542-0.189-0.36220.49050.38360.15940.072-0.07510.15840.2395-0.0679-0.01980.3429-0.01610.2105-19.323732.271228.6405
74.5089-0.47082.02293.62240.09374.7444-0.0766-0.14420.17510.3247-0.044-0.1062-0.0641-0.15860.12060.0566-0.06840.01210.2025-0.03710.0622-13.976342.124129.6526
80.71620.60741.41893.45595.248622.9269-0.18490.14260.4894-0.3277-0.65780.1917-0.6598-0.60270.84270.0649-0.0159-0.08890.30630.09650.4073-11.938748.126825.6291
96.76540.62922.48852.1743-0.38765.17590.07270.0159-0.58690.2133-0.1432-0.31790.46410.42050.07060.1174-0.02730.04790.1904-0.03410.1848-9.041236.296333.3144
107.4371-0.31370.13692.2196-1.63742.86210.4807-0.6443-0.27220.6781-0.3363-0.28960.21050.5281-0.14440.6346-0.0036-0.08050.50770.06350.6433-1.154932.162243.6015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 73
2X-RAY DIFFRACTION2A74 - 87
3X-RAY DIFFRACTION3A88 - 184
4X-RAY DIFFRACTION4A185 - 231
5X-RAY DIFFRACTION5A232 - 244
6X-RAY DIFFRACTION6B32 - 51
7X-RAY DIFFRACTION7B52 - 108
8X-RAY DIFFRACTION8B109 - 126
9X-RAY DIFFRACTION9B127 - 185
10X-RAY DIFFRACTION10B186 - 243

+
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