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- PDB-4oia: Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Grou... -

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Basic information

Entry
Database: PDB / ID: 4oia
TitleCrystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group P4322
ComponentsIntercellular adhesion molecule 5
KeywordsCELL ADHESION / ICAM-5 extracellular domain / IgV / inmunology / ICAM-5 / Brain
Function / homology
Function and homology information


regulation of synapse assembly / Integrin cell surface interactions / phagocytosis / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / glutamatergic synapse / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Intercellular adhesion molecule 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsRecacha, R. / Jimenez, D. / Tian, L. / Barredo, R. / Ghamberg, C. / Casasnovas, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal structures of an ICAM-5 ectodomain fragment show electrostatic-based homophilic adhesions.
Authors: Recacha, R. / Jimenez, D. / Tian, L. / Barredo, R. / Gahmberg, C.G. / Casasnovas, J.M.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intercellular adhesion molecule 5
B: Intercellular adhesion molecule 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,74319
Polymers82,6232
Non-polymers6,12017
Water0
1
A: Intercellular adhesion molecule 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,48410
Polymers41,3121
Non-polymers3,1729
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intercellular adhesion molecule 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2599
Polymers41,3121
Non-polymers2,9488
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 96.070, 321.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Intercellular adhesion molecule 5 / / ICAM-5 / Telencephalin


Mass: 41311.652 Da / Num. of mol.: 2 / Fragment: D1-D4, unp residues 32-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM5, TLCN, TLN / Production host: homo sapiens (human) / References: UniProt: Q9UMF0
#2: 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.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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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: 4.17 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris-HCl 8.5, 10% PEG4000 , VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.7→25 Å / Num. all: 16867 / Num. obs: 16867 / % possible obs: 99.8 % / Observed criterion σ(F): 30578 / Observed criterion σ(I): 30578

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→24.992 Å / SU ML: 0.47 / σ(F): 1.14 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 856 5.11 %
Rwork0.23 --
obs0.2326 16830 99.64 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→24.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 401 0 6125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036274
X-RAY DIFFRACTIONf_angle_d0.7348558
X-RAY DIFFRACTIONf_dihedral_angle_d19.9442372
X-RAY DIFFRACTIONf_chiral_restr0.0481032
X-RAY DIFFRACTIONf_plane_restr0.0031102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.8190.37661710.30482586X-RAY DIFFRACTION100
3.819-3.9550.36161440.28142631X-RAY DIFFRACTION100
3.955-4.11270.36621550.28162647X-RAY DIFFRACTION100
4.1127-4.2990.28721600.25792620X-RAY DIFFRACTION100
4.299-4.52440.28231150.21922643X-RAY DIFFRACTION100
4.5244-4.8060.2511440.19192660X-RAY DIFFRACTION100
4.806-5.1740.21281430.17782596X-RAY DIFFRACTION100
5.174-5.68910.2931260.19232693X-RAY DIFFRACTION100
5.6891-6.49970.28441510.21582612X-RAY DIFFRACTION100
6.4997-8.14160.27821270.22372640X-RAY DIFFRACTION100
8.1416-24.99290.2191240.2372629X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8337-0.25594.61638.72930.84993.86360.3405-0.61530.09350.7861-0.25950.41221.4570.4484-0.00111.003-0.11310.11050.9767-0.020.69517.438556.92653.6079
23.7331-2.8564-2.25594.20273.34273.75170.1940.4107-0.1442-0.39020.3154-0.5278-0.3404-0.2175-0.43881.1048-0.2436-0.00591.1756-0.09280.75824.620539.85417.2592
35.94320.1236-1.82418.63851.96235.22651.09010.63720.38710.1908-0.54720.1225-1.0726-0.297-0.61411.5860.01330.1771.47-0.06830.801830.893137.4297-27.5447
42.1463-0.09572.21810.7022-0.5192.68961.01843.58450.3215-1.5156-0.20320.6589-1.6484-3.19710.0953.00550.88780.08074.48030.20071.312736.957335.6161-68.8604
57.3193-0.55472.50478.37581.52447.6744-0.20880.4812-0.1952-1.44470.34820.95320.616-0.528-0.44581.16010.0809-0.21191.35020.09070.8446-7.654732.851722.5103
64.1011-0.59690.27524.934-2.0557.5952-0.2687-0.1083-0.02590.79330.0566-0.4510.1764-0.6470.21920.9479-0.1372-0.11921.13120.04190.69879.817524.768158.3561
79.1213-1.1684-0.73238.64270.37075.4148-0.3939-0.2857-0.20680.04370.41750.41020.32520.8684-0.01460.9065-0.1045-0.14280.84950.09380.641612.756717.0261102.7355
81.625-0.5667-2.00163.16893.184.37220.7775-1.56630.37272.8438-0.2857-0.053-1.3706-1.3855-0.51673.88150.62650.32922.3782-0.00911.318117.37311.4798143.9312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:85 )A1 - 85
2X-RAY DIFFRACTION2( CHAIN A AND RESID 86:194 )A86 - 194
3X-RAY DIFFRACTION3( CHAIN A AND RESID 195:289 )A195 - 289
4X-RAY DIFFRACTION4( CHAIN A AND RESID 290:374 )A290 - 374
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:85 )B1 - 85
6X-RAY DIFFRACTION6( CHAIN B AND RESID 86:194 )B86 - 194
7X-RAY DIFFRACTION7( CHAIN B AND RESID 195:289 )B195 - 289
8X-RAY DIFFRACTION8( CHAIN B AND RESID 290:375 )B290 - 375

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