[English] 日本語
Yorodumi
- PDB-5wb2: US28 bound to engineered chemokine CX3CL1.35 and nanobodies -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wb2
TitleUS28 bound to engineered chemokine CX3CL1.35 and nanobodies
Components
  • CX3CL1 protein
  • Envelope protein US28, nanobody 7 fusion protein
  • nanobody B1
KeywordsMEMBRANE PROTEIN / chemokine receptor / engineered proteins
Function / homology
Function and homology information


CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / negative regulation of glutamate receptor signaling pathway / autocrine signaling / lymphocyte chemotaxis / synapse pruning ...CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / negative regulation of glutamate receptor signaling pathway / autocrine signaling / lymphocyte chemotaxis / synapse pruning / positive regulation of microglial cell migration / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of microglial cell activation / negative regulation of neuron migration / positive regulation of transforming growth factor beta1 production / CCR chemokine receptor binding / microglial cell proliferation / positive regulation of actin filament bundle assembly / leukocyte migration involved in inflammatory response / C-C chemokine receptor activity / integrin activation / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / leukocyte chemotaxis / angiogenesis involved in wound healing / chemokine activity / Chemokine receptors bind chemokines / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / macrophage chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / regulation of neurogenesis / negative regulation of tumor necrosis factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of cell-substrate adhesion / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of cell migration / response to ischemia / cell projection / cell chemotaxis / positive regulation of smooth muscle cell proliferation / microglial cell activation / calcium-mediated signaling / defense response / cytokine-mediated signaling pathway / cell-cell adhesion / regulation of synaptic plasticity / positive regulation of neuron projection development / neuron cellular homeostasis / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of angiogenesis / chemotaxis / integrin binding / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / neuron projection / cell adhesion / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / viral envelope / negative regulation of apoptotic process / perinuclear region of cytoplasm / host cell plasma membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
CX3C chemokine domain / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Rhopdopsin 7-helix transmembrane proteins ...CX3C chemokine domain / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / G-protein coupled receptor homolog US28 / Fractalkine / CX3CL1 protein / Envelope protein US28
Similarity search - Component
Biological speciesHuman cytomegalovirus
Lama glama (llama)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJude, K.M. / Burg, J.S. / Tsutsumi, N. / Miles, T.F. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097015 United States
CitationJournal: Elife / Year: 2018
Title: Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy.
Authors: Miles, T.F. / Spiess, K. / Jude, K.M. / Tsutsumi, N. / Burg, J.S. / Ingram, J.R. / Waghray, D. / Hjorto, G.M. / Larsen, O. / Ploegh, H.L. / Rosenkilde, M.M. / Garcia, K.C.
History
DepositionJun 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jan 1, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope protein US28, nanobody 7 fusion protein
B: CX3CL1 protein
D: nanobody B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,40111
Polymers74,9413
Non-polymers2,4608
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-45 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 128.940, 127.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules B

#2: Protein CX3CL1 protein / engineered chemokine CX3CL1.35


Mass: 8631.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CX3CL1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6I9S9, UniProt: P78423*PLUS

-
Antibody , 2 types, 2 molecules AD

#1: Antibody Envelope protein US28, nanobody 7 fusion protein / US28 protein


Mass: 52158.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus, (gene. exp.) Lama glama (llama)
Gene: US28 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q80KM9, UniProt: P69333*PLUS
#3: Antibody nanobody B1


Mass: 14151.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: MES pH 6.0, 50 mM lithium sulfate, 35-39% PEG300, 1% 1,2,3-heptanetriol in monoolein:cholesterol (9:1)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 7, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 10361 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 65.336 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.0289 / Net I/σ(I): 5.24
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 762 / CC1/2: 0.506 / Rrim(I) all: 1.395 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMay 1, 2016data reduction
XSCALEMay 1, 2016data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XT1

4xt1


Resolution: 3.5→45.374 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 1041 10.08 %random selection
Rwork0.252 ---
obs0.2563 10332 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→45.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4755 0 152 0 4907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035029
X-RAY DIFFRACTIONf_angle_d0.7016848
X-RAY DIFFRACTIONf_dihedral_angle_d10.1162923
X-RAY DIFFRACTIONf_chiral_restr0.04788
X-RAY DIFFRACTIONf_plane_restr0.004838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.68470.33011470.321310X-RAY DIFFRACTION100
3.6847-3.91540.37361510.29871298X-RAY DIFFRACTION99
3.9154-4.21750.351410.27861287X-RAY DIFFRACTION100
4.2175-4.64160.26561580.22811314X-RAY DIFFRACTION100
4.6416-5.31240.29351510.22381321X-RAY DIFFRACTION99
5.3124-6.68960.33491440.27571343X-RAY DIFFRACTION99
6.6896-45.37730.23711490.22621418X-RAY DIFFRACTION98

+
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