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

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Basic information

Entry
Database: PDB / ID: 2jcr
TitleThe hyaluronan binding domain of murine CD44 in a Type B complex with an HA 8-mer
ComponentsCD44 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / POLYMORPHISM / BLOOD GROUP ANTIGEN / ALTERNATIVE SPLICING / 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 degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / 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 / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process / positive regulation of adaptive immune response / branching involved in prostate gland morphogenesis / 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 / plasma membrane
Similarity search - Function
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
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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.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.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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 82.100, 32.400
Angle α, β, γ (deg.)90.00, 118.00, 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 / Variant (production host): DE3 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.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growpH: 8
Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5 MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% ...Details: CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5 MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Jul 4, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.6 Å / Num. obs: 9641 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.6 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUMdata reduction
SAINTdata reduction
SADABSdata scaling
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JCQ

2jcq


Resolution: 2→28.61 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.443 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 407 4.8 %RANDOM
Rwork0.175 ---
obs0.179 8114 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0.88 Å2
2--0.78 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 99 134 1405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211390
X-RAY DIFFRACTIONr_bond_other_d0.0020.02891
X-RAY DIFFRACTIONr_angle_refined_deg1.282.021918
X-RAY DIFFRACTIONr_angle_other_deg0.8553.0062170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98924.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05915204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.704158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined0.1960.2245
X-RAY DIFFRACTIONr_nbd_other0.1950.21014
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2690
X-RAY DIFFRACTIONr_nbtor_other0.0810.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.51045
X-RAY DIFFRACTIONr_mcbond_other0.1641.5321
X-RAY DIFFRACTIONr_mcangle_it0.75521319
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3823662
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1614.5599
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.71132761
X-RAY DIFFRACTIONr_sphericity_free3.043134
X-RAY DIFFRACTIONr_sphericity_bonded0.92332238
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 12 -
Rwork0.203 367 -
obs--52.28 %
Refinement TLS params.Method: refined / Origin x: 2.465 Å / Origin y: -1.304 Å / Origin z: 2.78 Å
111213212223313233
T-0.1512 Å20.0124 Å20.0058 Å2--0.1324 Å2-0.0121 Å2---0.127 Å2
L2.219 °20.6752 °20.5528 °2-1.9063 °2-0.4115 °2--2.6616 °2
S0.0666 Å °-0.0367 Å °-0.033 Å °0.1476 Å °-0.0374 Å °-0.2054 Å °0.0202 Å °0.118 Å °-0.0292 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 174
2X-RAY DIFFRACTION1A - C1174 - 1181

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