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- PDB-2box: EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, i... -

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Basic information

Entry
Database: PDB / ID: 2box
TitleEGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with strontium.
ComponentsEGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR
KeywordsIMMUNE SYSTEM / CD97 / CD55 / 7TM / CALCIUM-BINDING / CELL ADHESION / EGF-LIKE DOMAIN / G-PROTEIN COUPLED RECEPTOR
Function / homology
Function and homology information


granulocyte chemotaxis / chondroitin sulfate binding / regulation of mast cell degranulation / leading edge membrane / Class B/2 (Secretin family receptors) / G protein-coupled receptor activity / ruffle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell migration / cell surface receptor signaling pathway ...granulocyte chemotaxis / chondroitin sulfate binding / regulation of mast cell degranulation / leading edge membrane / Class B/2 (Secretin family receptors) / G protein-coupled receptor activity / ruffle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell migration / cell surface receptor signaling pathway / cell adhesion / G protein-coupled receptor signaling pathway / inflammatory response / calcium ion binding / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site ...GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / Laminin / Laminin / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / STRONTIUM ION / Adhesion G protein-coupled receptor E2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAbbott, R.J.M. / Spendlove, I. / Roversi, P. / Teriete, P. / Knott, V. / Handford, P.A. / McDonnell, J.M. / Lea, S.M.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural and Functional Characterization of a Novel T Cell Receptor Co-Regulatory Protein Complex, Cd97-Cd55.
Authors: Abbott, R.J.M. / Spendlove, I. / Roversi, P. / Fitzgibbon, H. / Knott, V. / Teriete, P. / Mcdonnell, J.M. / Handford, P.A. / Lea, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Three Egf Domains of Emr2, a 7Tm Immune-System Molecule
Authors: Abbott, R.J.M. / Knott, V. / Roversi, P. / Neudeck, S. / Lukacik, P. / Handford, P.A. / Lea, S.M.
History
DepositionApr 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9415
Polymers15,5931
Non-polymers3484
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.106, 61.575, 35.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR / EGF-LIKE MODULE EMR2


Mass: 15593.094 Da / Num. of mol.: 1 / Fragment: EGF DOMAINS 1,2 AND 5,RESIDUES 25-118,212-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / Variant (production host): PREP4 / References: UniProt: Q9UHX3
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS PDB DESCIBES THE ALTERNATIVELY SPLICED ISOFORM C OF THE GENE ID 30817 LOCUS TAG HGNC3337 OMIM 606100

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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: 3.2 Å3/Da / Density % sol: 61.2 %
Crystal growpH: 6.5
Details: 0.1 M STRONTIUM CHLORIDE, 12-16% W/V PEG 8000, 0.1 M NA CACODYLATE BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→23.26 Å / Num. obs: 8270 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 0.083 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)

2bou


Resolution: 2.5→23.262 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO.DAT / Details: REFINED USING BUSTER-TNT VERSION 1.0.4
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 373 5 %RANDOM
Rwork0.2403 ---
all0.2426 7342 --
obs0.2426 7342 --
Solvent computationSolvent model: BABINET MASKING / Bsol: 30.4 Å2 / ksol: 0.407 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→23.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 8 94 1116
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00310552
X-RAY DIFFRACTIONt_angle_deg0.64114273
X-RAY DIFFRACTIONt_dihedral_angle_d17.7656200
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005332
X-RAY DIFFRACTIONt_gen_planes0.0121515
X-RAY DIFFRACTIONt_it0.778105620
X-RAY DIFFRACTIONt_nbd0.035235
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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