[English] 日本語
Yorodumi
- PDB-3bn3: crystal structure of ICAM-5 in complex with aL I domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bn3
Titlecrystal structure of ICAM-5 in complex with aL I domain
Components
  • Integrin alpha-L
  • Intercellular adhesion molecule 5
KeywordsCell adhesion / immune system / ICAM-5 / I domain / integrin / allosteric mobility
Function / homology
Function and homology information


memory T cell extravasation / 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 / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / leukocyte cell-cell adhesion ...memory T cell extravasation / 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 / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / glutamatergic synapse / Neutrophil degranulation / cell surface / signal transduction / 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 / von Willebrand factor type A domain / Immunoglobulin 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 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 / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin alpha-L / Intercellular adhesion molecule 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.099 Å
AuthorsZhang, H. / Springer, T.A. / Wang, J.-h.
CitationJournal: Mol.Cell / Year: 2008
Title: An unusual allosteric mobility of the C-terminal helix of a high-affinity alpha L integrin I domain variant bound to ICAM-5
Authors: Zhang, H. / Casasnovas, J.M. / Jin, M. / Liu, J.H. / Gahmberg, C.G. / Springer, T.A. / Wang, J.-h.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: 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 / Database references / 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_conn_type / struct_ref_seq_dif / 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.conn_type_id / _struct_conn.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_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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 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
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-L
B: Intercellular adhesion molecule 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,16610
Polymers42,6482
Non-polymers1,5188
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint10 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.793, 71.507, 143.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain / CD11a antigen


Mass: 20532.496 Da / Num. of mol.: 1 / Fragment: I domain / Mutation: F265S, F292G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#2: Protein Intercellular adhesion molecule 5 / / ICAM-5 / Telencephalin


Mass: 22115.334 Da / Num. of mol.: 1 / Fragment: N-terminal, two domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM5, TLCN, TLN / Plasmid: pBJ5-GS / Cell (production host): Hampster Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): lec 3.2.8.1 / Tissue (production host): ovary / References: UniProt: Q9UMF0

-
Sugars , 2 types, 5 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.: 1
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
#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 / 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

-
Non-polymers , 3 types, 229 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 7.5%PEG8000, 10%glycerol, 5mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.099→71.98 Å / Num. obs: 37303 / % possible obs: 98.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.054
Reflection shellResolution: 2.099→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.76 / Num. unique all: 3564 / Rsym value: 0.471 / % possible all: 95.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.3.0026refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementStarting model: PDB IDS 1T0P AND 1IC1
Resolution: 2.099→71.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.384 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1863 5 %RANDOM
Rwork0.191 ---
all0.193 37303 --
obs0.193 37303 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.703 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--4.05 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.099→71.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 97 226 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223167
X-RAY DIFFRACTIONr_bond_other_d0.0010.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.322.0024283
X-RAY DIFFRACTIONr_angle_other_deg0.8163.0025420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18922.69145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28515540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6361533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
X-RAY DIFFRACTIONr_nbd_refined0.2010.2497
X-RAY DIFFRACTIONr_nbd_other0.1890.22292
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21492
X-RAY DIFFRACTIONr_nbtor_other0.10.21744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2182
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.29
X-RAY DIFFRACTIONr_mcbond_it2.85552439
X-RAY DIFFRACTIONr_mcbond_other0.5315753
X-RAY DIFFRACTIONr_mcangle_it3.484103027
X-RAY DIFFRACTIONr_scbond_it2.70951471
X-RAY DIFFRACTIONr_scangle_it4.104101256
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 134 -
Rwork0.261 2492 -
all-2626 -
obs--95.08 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2786-0.41260.28979.32612.59473.2681-0.0511-0.46070.20870.61530.3843-0.88240.39110.7099-0.3332-0.30630.0208-0.0790.0185-0.1223-0.0761-13.374-7.446740.5065
23.0865-0.8144-1.02734.02241.84143.69030.0717-0.23350.6265-0.09770.1168-0.3636-0.3380.189-0.1885-0.1865-0.05210.0067-0.2055-0.07380.0047-18.0757-1.201834.1248
36.05532.5312-0.283317.5310.57063.85650.0872-0.1905-0.2262-0.56320.359-1.6492-0.00290.9762-0.4462-0.4889-0.04050.1434-0.0097-0.16030.0715-5.0674-10.947129.0331
414.8948-5.55313.46413.41984.5325.9190.4120.29490.59841.52430.12770.29-0.7854-0.2675-0.53960.01720.12950.01970.41270.42440.509-1.1366-31.80436.2154
50.1215-0.0689-0.53476.1054-3.99385.39630.3135-0.2247-0.4246-0.30210.30970.73240.4806-0.5948-0.6231-0.09750.01120.0136-0.03290.0796-0.0356-26.5476-33.142531.112
62.9984-0.66863.56537.5962-0.4688.56320.06550.3243-0.0852-0.7275-0.1892-0.0660.24270.35120.1237-0.14360.04350.102-0.09940.0385-0.2035-20.5993-29.004921.9585
70.1521-0.88750.71255.2831-3.283110.6552-0.1498-0.16240.19290.1642-0.0242-0.1151-0.6559-0.34640.1739-0.1249-0.07080.0363-0.10860.0362-0.0585-24.3973-25.984930.8679
81.20840.0132.36380.08730.333519.6866-0.0555-0.16720.10890.02730.0034-0.3068-0.45060.39780.0521-0.01390.0027-0.0789-0.04910.0003-0.1769-19.7186-37.540270.4138
92.46150.41272.50880.0840.44598.85160.0399-0.4655-0.05210.1646-0.0585-0.0923-0.1218-0.58120.0186-0.06790.0581-0.0417-0.1502-0.0066-0.2441-27.5334-39.829563.2714
103.17090.14167.25324.81143.663237.37590.1935-0.52910.0340.6629-0.0408-0.06171.41540.615-0.1528-0.1296-0.0015-0.08980.05780.0256-0.1684-18.8366-43.123477.5868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA128 - 1601 - 33
2X-RAY DIFFRACTION2AA161 - 25134 - 124
3X-RAY DIFFRACTION3AA252 - 292125 - 165
4X-RAY DIFFRACTION4AA293 - 307166 - 180
5X-RAY DIFFRACTION5BB1 - 211 - 21
6X-RAY DIFFRACTION6BB22 - 5422 - 54
7X-RAY DIFFRACTION7BB55 - 8555 - 85
8X-RAY DIFFRACTION8BB86 - 11286 - 112
9X-RAY DIFFRACTION9BB113 - 181113 - 181
10X-RAY DIFFRACTION10BB182 - 196182 - 196

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more