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- PDB-2jcq: The hyaluronan binding domain of murine CD44 in a Type A complex ... -

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Basic information

Entry
Database: PDB / ID: 2jcq
TitleThe hyaluronan binding domain of murine CD44 in a Type A complex with an HA 8-mer
ComponentsCD44 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / BLOOD GROUP ANTIGEN / LECTIN / ANTIGEN / MEMBRANE / RECEPTOR / SULFATION / GLYCOPROTEIN / C-TYPE LECTIN / CELL ADHESION / EXTRACELLULAR MATRIX / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / SUGAR- BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / Integrin cell surface interactions / hyaluronan catabolic process ...Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Cell surface interactions at the vascular wall / Integrin cell surface interactions / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / channel regulator activity / cargo receptor activity / wound healing, spreading of cells / cytokine receptor activity / branching involved in ureteric bud morphogenesis / epidermal growth factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / Wnt signaling pathway / negative regulation of inflammatory response / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / apical plasma membrane / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBanerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structures of the Cd44-Hyaluronan Complex Provide Insight Into a Fundamental Carbohydrate-Protein Interaction.
Authors: Banerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
History
DepositionJan 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_assembly_gen / 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_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.occupancy / _atom_site.type_symbol / _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.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD44 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5803
Polymers17,1291
Non-polymers1,4512
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.794, 82.051, 32.278
Angle α, β, γ (deg.)90.00, 117.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD44 ANTIGEN / PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE ...PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR / HERMES ANTIGEN / HYALURONATE RECEPTOR / LYMPHOCYTE ANTIGEN LY-24 / CD44


Mass: 17129.047 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174
Source method: isolated from a genetically manipulated source
Details: ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL RESIDUES M, N ADDED AT THE N-TERMINUS
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P15379
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1359.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5]/1-2-1-2-1-2-1/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 7
Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) ...Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT EITHER PH 7.0 OR PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.25→23.42 Å / Num. obs: 36225 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 5.44 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.75
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.77 / % possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUH

1uuh


Resolution: 1.25→41.03 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.234 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.156 1945 5.1 %RANDOM
Rwork0.13 ---
obs0.132 36568 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.26 Å2
2---0.15 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 99 175 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211382
X-RAY DIFFRACTIONr_bond_other_d0.0020.021162
X-RAY DIFFRACTIONr_angle_refined_deg1.7742.0221907
X-RAY DIFFRACTIONr_angle_other_deg0.8632710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88724.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84115203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.856158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021521
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02267
X-RAY DIFFRACTIONr_nbd_refined0.2370.2259
X-RAY DIFFRACTIONr_nbd_other0.1950.21254
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2714
X-RAY DIFFRACTIONr_nbtor_other0.0850.2855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7181.51015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12921311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.23653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0644.5596
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 158
Rwork0.211 2622
Refinement TLS params.Method: refined / Origin x: 2.324 Å / Origin y: -1.311 Å / Origin z: 2.869 Å
111213212223313233
T-0.0352 Å2-0.0049 Å20.0002 Å2--0.0256 Å2-0.0011 Å2---0.0201 Å2
L0.741 °2-0.0363 °20.1673 °2-0.5171 °2-0.0496 °2--1.2897 °2
S0.0061 Å °-0.0019 Å °0.0249 Å °0.0152 Å °-0.015 Å °-0.049 Å °-0.0236 Å °0.0404 Å °0.0089 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 1699
2X-RAY DIFFRACTION1A1175 - 1181

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