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- PDB-4oib: Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group R3 -

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Basic information

Entry
Database: PDB / ID: 4oib
TitleCrystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group R3
ComponentsIntercellular adhesion molecule 5
KeywordsCELL ADHESION / cell surface / neurons / immunoglobulin superfamily / intercellular adhesion molecules / ICAM-5 / telencephalin
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: 3.503 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,61610
Polymers41,3121
Non-polymers4,3049
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)228.560, 228.560, 69.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 41311.652 Da / Num. of mol.: 1 / Fragment: D1-D4
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 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.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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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: 8.52 Å3/Da / Density % sol: 85.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.6
Details: 100 mM sodium acetate, 10% PEG 4000, VAPOR DIFFUSION, temperature 294K, pH 5.6

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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
Reflection twinOperator: k,h,-l / Fraction: 0.08
ReflectionResolution: 3.5→25 Å / Num. obs: 15373 / % possible obs: 99.8 %

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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: 3.503→24.938 Å / σ(F): 1.99 / Phase error: 38.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2733 1708 10 %
Rwork0.2424 --
obs0.2444 15373 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→24.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 284 0 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043191
X-RAY DIFFRACTIONf_angle_d1.0654367
X-RAY DIFFRACTIONf_dihedral_angle_d25.6911301
X-RAY DIFFRACTIONf_chiral_restr0.06548
X-RAY DIFFRACTIONf_plane_restr0.003546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5051-3.56530.45341760.41791512X-RAY DIFFRACTION90
3.5653-3.630.40181740.40621534X-RAY DIFFRACTION90
3.63-3.69960.39991640.37891618X-RAY DIFFRACTION91
3.6996-3.77480.38961640.35721436X-RAY DIFFRACTION90
3.7748-3.85660.36661780.35371570X-RAY DIFFRACTION90
3.8566-3.9460.33471760.32031566X-RAY DIFFRACTION90
3.946-4.04430.3291680.32571514X-RAY DIFFRACTION90
4.0443-4.15310.35561640.33051476X-RAY DIFFRACTION90
4.1531-4.27480.37051780.31241600X-RAY DIFFRACTION90
4.2748-4.4120.2841680.29341560X-RAY DIFFRACTION90
4.412-4.56880.35491740.27221496X-RAY DIFFRACTION90
4.5688-4.75050.2761740.25011564X-RAY DIFFRACTION90
4.7505-4.96510.24561760.25311540X-RAY DIFFRACTION90
4.9651-5.22460.28421680.23991492X-RAY DIFFRACTION90
5.2246-5.54860.29491680.25161546X-RAY DIFFRACTION90
5.5486-5.97150.30461740.25541556X-RAY DIFFRACTION90
5.9715-6.56250.27471560.2491526X-RAY DIFFRACTION91
6.5625-7.48960.24571780.22481538X-RAY DIFFRACTION90
7.4896-9.35260.20821720.16751518X-RAY DIFFRACTION90
9.3526-24.93820.20091640.14761536X-RAY DIFFRACTION89
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)
17.4849-2.6786-0.77318.57982.59375.2629-0.1495-0.04180.48551.61110.0528-0.09042.23550.8010.12722.2010.1023-0.251.3151-0.21231.0938207.441150.868684.1111
25.72813.87990.26624.16363.60018.6049-0.1924-0.3875-0.18371.3334-0.36230.53080.7692-0.23660.61841.79190.2228-0.18350.9672-0.16051.3574212.678717.437262.9399
38.46515.18331.8469.5444-2.69642.70570.51040.1540.5866-0.3431-0.02981.1585-0.25740.1828-0.26211.5669-0.01760.51381.3867-0.61741.2165199.8416-23.154149.5692
41.50811.56270.80118.8426-0.30136.25580.4604-0.4145-0.44911.1741-0.12131.114-0.6276-0.4768-0.22741.4237-0.15240.25411.4185-0.36131.2045189.277-61.961243.3795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 1:85)
2X-RAY DIFFRACTION2(chain 'A' and resseq 86:193)
3X-RAY DIFFRACTION3(chain 'A' and resseq 194:289)
4X-RAY DIFFRACTION4(chain 'A' and resseq 290:372)

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