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- PDB-2bo2: 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: 2bo2
TitleEGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with calcium.
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, 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 / Adhesion G protein-coupled receptor E2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 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 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4837
Polymers31,1862
Non-polymers2975
Water57632
1
A: EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8104
Polymers15,5931
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6733
Polymers15,5931
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.845, 61.377, 35.584
Angle α, β, γ (deg.)90.00, 84.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.88169, -0.01375, -0.47163), (0.02917, -0.99925, -0.0254), (-0.47093, -0.03615, 0.88143)40.71574, 3.80116, 0.42833
2given(-0.89028, -0.01871, -0.45502), (0.02905, -0.99945, -0.01575), (-0.45448, -0.02724, 0.89034)0.87519, 3.83622, 0.35158
3given(-0.87053, -0.02242, -0.49161), (0.04851, -0.99801, -0.04038), (-0.48973, -0.05901, 0.86988)1.04546, 3.89819, 0.70579
4given(-0.87811, -0.04456, -0.47638), (0.06446, -0.99759, -0.0255), (-0.4741, -0.0531, 0.87887)40.72758, 3.449, 0.32825
5given(-0.87421, -0.04832, -0.48314), (0.06119, -0.99807, -0.01089), (-0.48168, -0.03908, 0.87547)40.74611, 3.40166, 0.72657

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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.: 2 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS IS NCBI PROTSEQ ENTRY NP_690881 IT IS ALTERNATIVELY SPLICED ISOFORM C OF THE GENE ID 30817 ...THIS IS NCBI PROTSEQ ENTRY NP_690881 IT IS ALTERNATIVELY SPLICED ISOFORM C OF THE GENE ID 30817 LOCUS TAG HGNC3337 OMIM 606100. THE ENTRY BELOW DESCRIBES EGF DOMAINS 1, 2 AND 5.

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growpH: 6.5
Details: 0.1-0.175 M CALCIUM ACETATE, 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: 2.6→29.5 Å / Num. obs: 10840 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: -4.823 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
TNT5F.0.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)

2bou


Resolution: 2.6→29.54 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
Rfree0.26 516 5 %RANDOM
Rwork0.238 ---
all0.239 10174 --
obs0.239 10714 --
Solvent computationSolvent model: BABINET MASKING / Bsol: 47 Å2 / ksol: 0.3634 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 9 32 2125
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00321512
X-RAY DIFFRACTIONt_angle_deg0.55529143
X-RAY DIFFRACTIONt_dihedral_angle_d19.79112800
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004642
X-RAY DIFFRACTIONt_gen_planes0.0113115
X-RAY DIFFRACTIONt_it0.829215120
X-RAY DIFFRACTIONt_nbd0.03525
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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