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- PDB-9ejw: MCMV immunoevasin m11 binding murine CD44 -

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Basic information

Entry
Database: PDB / ID: 9ejw
TitleMCMV immunoevasin m11 binding murine CD44
Components
  • CD44 antigen
  • M11 protein
KeywordsVIRAL PROTEIN / Immunoevasin / Complex / Cytomegalovirus
Function / homology
Function and homology information


Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / Integrin cell surface interactions / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process ...Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / Integrin cell surface interactions / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process / branching involved in prostate gland morphogenesis / positive regulation of adaptive immune response / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / channel regulator activity / negative regulation of CD4-positive, alpha-beta T cell proliferation / wound healing, spreading of cells / cargo receptor activity / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / membrane raft / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Gp34-like superfamily / Immune evasion protein / Immune evasion protein / CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) ...Gp34-like superfamily / Immune evasion protein / Immune evasion protein / CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
CYSTEINE / M11 protein / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murid betaherpesvirus 1 (Murine cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDeuss, F.A. / Rossjohn, J. / Sng, X.Y.X. / Voigt, V. / Schuster, I.S. / Fleming, P. / Abuwarwar, M. / van Dommelen, S. / Neate, G. / Horsnell, H.L. ...Deuss, F.A. / Rossjohn, J. / Sng, X.Y.X. / Voigt, V. / Schuster, I.S. / Fleming, P. / Abuwarwar, M. / van Dommelen, S. / Neate, G. / Horsnell, H.L. / Golzarroshan, B. / Varelias, A. / Hill, G.R. / Lyman, S.D. / Mueller, S.N. / Scalzo, A.A. / Wikstrom, M.E. / Berry, R. / Fletcher, A.L. / Andoniou, C.E. / Degli-Esposti, M.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nature / Year: 2026
Title: Fibroblastic reticular cells control the initiation of adaptive T cell responses via CD44
Authors: Sng, X.Y.X. / Voigt, V. / Schuster, I.S. / Fleming, P. / Deuss, F.A. / Abuwarwar, M.H. / van Dommelen, S. / Neate, G. / Arnold, R.M. / Horsnell, H.L. / Daly, S. / Golzarroshan, B. / ...Authors: Sng, X.Y.X. / Voigt, V. / Schuster, I.S. / Fleming, P. / Deuss, F.A. / Abuwarwar, M.H. / van Dommelen, S. / Neate, G. / Arnold, R.M. / Horsnell, H.L. / Daly, S. / Golzarroshan, B. / Varelias, A. / Lyman, S.D. / Scalzo, A.A. / Hill, G.R. / Mueller, S.N. / Wikstrom, M.E. / Berry, R. / Rossjohn, J. / Fletcher, A.L. / Andoniou, C.E. / Degli-Esposti, M.A.
History
DepositionNov 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD44 antigen
B: M11 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,58610
Polymers33,7872
Non-polymers2,7998
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint12 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.839, 105.768, 112.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein CD44 antigen / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / ...Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Hermes antigen / Hyaluronate receptor / Lymphocyte antigen 24 / Ly-24 / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 17129.047 Da / Num. of mol.: 1 / Fragment: UNP residues 23-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P15379
#2: Protein M11 protein


Mass: 16658.160 Da / Num. of mol.: 1 / Fragment: UNP residues 28-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid betaherpesvirus 1 (Murine cytomegalovirus)
Strain: K181 / Gene: m11 / Production host: Baculoviridae (virus) / References: UniProt: A8E1J2

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Sugars , 4 types, 5 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][<C8N1O3>]{[(1+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 1
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
#7: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 411 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% w/v PEG3000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→47.9259 Å / Num. obs: 83341 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 12.4
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 1.613 / Num. unique obs: 83341 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.898 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 4197 5.04 %
Rwork0.1838 --
obs0.1847 83228 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 181 408 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072486
X-RAY DIFFRACTIONf_angle_d0.983438
X-RAY DIFFRACTIONf_dihedral_angle_d17.89971
X-RAY DIFFRACTIONf_chiral_restr0.078429
X-RAY DIFFRACTIONf_plane_restr0.006419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.3191490.29082597X-RAY DIFFRACTION100
1.4159-1.43260.28831430.28692571X-RAY DIFFRACTION100
1.4326-1.450.27081320.27722629X-RAY DIFFRACTION99
1.45-1.46840.28941400.26072569X-RAY DIFFRACTION100
1.4684-1.48770.28791210.25492589X-RAY DIFFRACTION100
1.4877-1.50810.29251410.24032630X-RAY DIFFRACTION100
1.5081-1.52970.25291400.23622566X-RAY DIFFRACTION99
1.5297-1.55250.21751480.22632580X-RAY DIFFRACTION100
1.5525-1.57680.23631400.21752619X-RAY DIFFRACTION100
1.5768-1.60260.22471610.21662568X-RAY DIFFRACTION99
1.6026-1.63020.22591320.20222586X-RAY DIFFRACTION100
1.6302-1.65990.22111590.20592639X-RAY DIFFRACTION100
1.6599-1.69180.21831390.19162571X-RAY DIFFRACTION100
1.6918-1.72630.19241500.19242607X-RAY DIFFRACTION100
1.7263-1.76390.23091390.19222633X-RAY DIFFRACTION100
1.7639-1.80490.18541100.18582621X-RAY DIFFRACTION100
1.8049-1.85010.18481400.18722652X-RAY DIFFRACTION100
1.8501-1.90010.19541310.19462602X-RAY DIFFRACTION100
1.9001-1.9560.1961250.17622670X-RAY DIFFRACTION100
1.956-2.01910.19181290.17332622X-RAY DIFFRACTION100
2.0191-2.09130.18241150.17752651X-RAY DIFFRACTION100
2.0913-2.1750.19751520.17522661X-RAY DIFFRACTION100
2.175-2.2740.17371600.17912605X-RAY DIFFRACTION100
2.274-2.39390.20251220.19152667X-RAY DIFFRACTION100
2.3939-2.54390.23111360.18882653X-RAY DIFFRACTION100
2.5439-2.74030.18721360.19122687X-RAY DIFFRACTION100
2.7403-3.0160.25031230.19012706X-RAY DIFFRACTION100
3.016-3.45230.18581590.16932690X-RAY DIFFRACTION100
3.4523-4.34910.17681530.14182739X-RAY DIFFRACTION100
4.3491-47.8980.19141720.17562851X-RAY DIFFRACTION100

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