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- PDB-2oz4: Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Su... -

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Basic information

Entry
Database: PDB / ID: 2oz4
TitleStructural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization
Components
  • FAB FRAGMENT LIGHT CHAIN
  • FAB FRAGMENT, HEAVY CHAIN
  • Intercellular adhesion molecule 1
KeywordsCELL ADHESION / IGSF DOMAIN / STRUCTURAL PLASTICITY / CELL-SURFACE DIMERIZATION
Function / homology
Function and homology information


regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte migration / leukocyte cell-cell adhesion / immunoglobulin complex / cell adhesion mediated by integrin / Interleukin-10 signaling / immunoglobulin mediated immune response / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / antigen binding / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / transmembrane signaling receptor activity / signaling receptor activity / virus receptor activity / : / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / 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 V-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 V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig heavy chain V region J558 / Intercellular adhesion molecule 1 / : / Intercellular adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, X. / Kim, T.D. / Carman, C.V. / Mi, L. / Song, G. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization.
Authors: Chen, X. / Kim, T.D. / Carman, C.V. / Mi, L.Z. / Song, G. / Springer, T.A.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_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 2.1Aug 30, 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 13, 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: Intercellular adhesion molecule 1
L: FAB FRAGMENT LIGHT CHAIN
H: FAB FRAGMENT, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,42612
Polymers75,0493
Non-polymers1,3779
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)185.396, 69.342, 88.173
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-2002-

ZN

21L-3081-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Intercellular adhesion molecule 1


Mass: 28682.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHINESE HAMSTER CHO.LEC3.2.8.1 / References: UniProt: Q5NKV7, UniProt: P05362*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody FAB FRAGMENT LIGHT CHAIN


Mass: 23592.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q58EU4
#3: Antibody FAB FRAGMENT, HEAVY CHAIN


Mass: 22773.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01757

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Sugars , 2 types, 3 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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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Non-polymers , 4 types, 282 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M LITHIUM SULFATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 26015 / Num. obs: 26015 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.543 / % possible all: 58.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1F11, 1P53

1f11

1p53


Resolution: 2.7→28.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 26.501 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R: 1.353 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2559 9.9 %RANDOM
Rwork0.204 ---
obs0.209 23400 100 %-
all-25959 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.34 Å2
Baniso -1Baniso -2Baniso -3
1--5.52 Å20 Å2-4.12 Å2
2--6.95 Å20 Å2
3----4.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.455 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 80 276 5590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225449
X-RAY DIFFRACTIONr_bond_other_d0.0010.023605
X-RAY DIFFRACTIONr_angle_refined_deg0.9031.9747446
X-RAY DIFFRACTIONr_angle_other_deg0.65638848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.965685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83124.72214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59915863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7881525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021008
X-RAY DIFFRACTIONr_nbd_refined0.1490.2864
X-RAY DIFFRACTIONr_nbd_other0.1640.23592
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22617
X-RAY DIFFRACTIONr_nbtor_other0.0770.22975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1530.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.62734460
X-RAY DIFFRACTIONr_mcbond_other0.01631373
X-RAY DIFFRACTIONr_mcangle_it0.897185624
X-RAY DIFFRACTIONr_scbond_it0.4932333
X-RAY DIFFRACTIONr_scangle_it0.865181822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 103 -
Rwork0.453 1090 -
obs--100 %
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)
13.7888-2.20242.58483.2977-1.63365.4443-0.1355-0.02560.6613-0.08650.0192-0.0697-0.70920.23890.1163-0.307-0.13570.0182-0.1784-0.0611-0.1192-64.156110.117262.9419
29.48232.56161.7373.7392-0.13135.39140.0955-0.26520.0824-0.0955-0.13830.30020.47060.15810.0429-0.2670.00050.0304-0.2413-0.0516-0.3925-64.1176-12.626265.1816
38.46337.67951.738613.12940.26893.81390.19650.44450.1005-0.99820.23121.7280.417-0.4469-0.42780.07440.0958-0.3244-0.22370.0040.2564-93.17292.257239.7835
45.27712.29672.250515.2083-4.924610.25090.21220.8065-0.823-2.5219-0.6196-1.10870.80450.45810.40730.26760.21030.0077-0.1861-0.12770.262-81.3958-9.200338.8526
54.40573.90932.80536.21014.85318.94680.10950.1975-0.1447-0.00380.0842-0.3011-0.07450.712-0.1937-0.1634-0.01710.08340.00790.0739-0.2157-43.1146-23.98815.8955
64.6420.91231.58221.1815.513339.537-0.4793-0.24720.7968-1.18520.0738-0.0566-3.81881.21550.40550.4421-0.250.0305-0.22610.0229-0.0754-38.6333-1.635339.7885
75.90261.1004-5.57811.10670.50248.60280.046-1.3023-0.17880.1845-0.05560.0272-0.05641.42730.0096-0.34950.0297-0.0340.4818-0.0217-0.2809-47.8775-6.465580.8953
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LB1 - 1081 - 108
2X-RAY DIFFRACTION2HC1 - 1141 - 114
3X-RAY DIFFRACTION3LB109 - 213109 - 213
4X-RAY DIFFRACTION4HC115 - 213115 - 213
5X-RAY DIFFRACTION5AA186 - 2821 - 97
6X-RAY DIFFRACTION6AA283 - 36698 - 181
7X-RAY DIFFRACTION7AA367 - 450182 - 265

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