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- PDB-1mq8: Crystal structure of alphaL I domain in complex with ICAM-1 -

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Basic information

Entry
Database: PDB / ID: 1mq8
TitleCrystal structure of alphaL I domain in complex with ICAM-1
Components
  • Integrin alpha-L
  • intercellular adhesion molecule-1
KeywordsIMMUNE SYSTEM / Ig superfamily / Rossmann fold / metal mediated protein interface
Function / homology
Function and homology information


regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / memory T cell extravasation / T cell antigen processing and presentation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / membrane to membrane docking ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / memory T cell extravasation / T cell antigen processing and presentation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / membrane to membrane docking / adhesion of symbiont to host / RUNX3 Regulates Immune Response and Cell Migration / establishment of endothelial barrier / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / receptor clustering / Interleukin-10 signaling / immunological synapse / Integrin cell surface interactions / specific granule membrane / phagocytosis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to leukemia inhibitory factor / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to glucose stimulus / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / integrin binding / virus receptor activity / signaling receptor activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / external side of plasma membrane / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / metal ion binding / 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 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 ...: / 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 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / Immunoglobulin domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Intercellular adhesion molecule 1 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsShimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. ...Shimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. / Wang, J.-H. / Springer, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structures of the aL I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation
Authors: Shimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. / Wang, J.-H. / Springer, T.A.
History
DepositionSep 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: intercellular adhesion molecule-1
B: Integrin alpha-L
C: intercellular adhesion molecule-1
D: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,26114
Polymers103,6304
Non-polymers2,63110
Water724
1
A: intercellular adhesion molecule-1
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1307
Polymers51,8152
Non-polymers1,3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint0 kcal/mol
Surface area20070 Å2
MethodPISA
2
C: intercellular adhesion molecule-1
D: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1307
Polymers51,8152
Non-polymers1,3165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint1 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.560, 62.868, 81.517
Angle α, β, γ (deg.)95.39, 106.67, 90.00
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Detailschain A and B form a biological complex, so do chain C and D. Chain A and C also form a biological dimer.

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein intercellular adhesion molecule-1 / / ICAM-1 / CD54 antigen / Major group rhinovirus receptor


Mass: 31623.771 Da / Num. of mol.: 2 / Fragment: domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM-1 / Plasmid: pMT/BiP/V5-His / Production host: Schneider S2 insect cells / Strain (production host): Schneider S2 insect cells / References: UniProt: P05362
#2: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / Leukocyte function associated molecule 1 / ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / Leukocyte function associated molecule 1 / alpha chain / CD11a


Mass: 20191.178 Da / Num. of mol.: 2 / Fragment: Integrin alphaL I domain / Mutation: L186C, F324C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LFA-1 (AlphaLbeta2) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20701

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Sugars , 2 types, 8 molecules

#3: 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.: 4
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
#4: 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 / N-Acetylglucosamine


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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Non-polymers , 2 types, 6 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
225 %PEG40001reservoir
30.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 25280 / Num. obs: 23330 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 7.7
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 1 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.5 / Num. unique all: 469 / Rsym value: 0.412 / % possible all: 70.7
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 50 Å / Num. obs: 12338 / Num. measured all: 23330
Reflection shell
*PLUS
% possible obs: 70.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IC1

1ic1


Resolution: 3.3→50 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood refinement target
RfactorNum. reflection% reflectionSelection details
Rfree0.313 577 5 %random
Rwork0.264 ---
all0.28 13251 --
obs0.28 11448 86.4 %-
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1--28.7 Å20.12 Å28.64 Å2
2--2 Å2-1.43 Å2
3---26.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.9 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 170 4 5854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015638
X-RAY DIFFRACTIONc_angle_deg1.74184
Refinement
*PLUS
Highest resolution: 3.3 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.7

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