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- PDB-3hi6: Crystal structure of intermediate affinity I domain of integrin L... -

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Basic information

Entry
Database: PDB / ID: 3hi6
TitleCrystal structure of intermediate affinity I domain of integrin LFA-1 with the Fab fragment of its antibody AL-57
Components
  • Heavy chain of Fab fragment of AL-57 against alpha L I domain
  • Integrin alpha-L
  • light chain of Fab fragment of AL-57 against alpha L I domain
Keywordscell adhesion/immune system / integrin / I domain / Fab / ligand mimetic antibody / cell adhesion / Alternative splicing / Calcium / Disulfide bond / Glycoprotein / Magnesium / Membrane / Polymorphism / Receptor / Transmembrane / cell adhesion-immune system COMPLEX
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / 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 / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. ...Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, H. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1.
Authors: Zhang, H. / Liu, J.H. / Yang, W. / Springer, T. / Shimaoka, M. / Wang, J.H.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Integrin alpha-L
B: Integrin alpha-L
H: Heavy chain of Fab fragment of AL-57 against alpha L I domain
L: light chain of Fab fragment of AL-57 against alpha L I domain
X: Heavy chain of Fab fragment of AL-57 against alpha L I domain
Y: light chain of Fab fragment of AL-57 against alpha L I domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,35914
Polymers134,6736
Non-polymers6868
Water12,611700
1
B: Integrin alpha-L
X: Heavy chain of Fab fragment of AL-57 against alpha L I domain
Y: light chain of Fab fragment of AL-57 against alpha L I domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6807
Polymers67,3363
Non-polymers3434
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-60 kcal/mol
Surface area26760 Å2
MethodPISA
2
A: Integrin alpha-L
H: Heavy chain of Fab fragment of AL-57 against alpha L I domain
L: light chain of Fab fragment of AL-57 against alpha L I domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6807
Polymers67,3363
Non-polymers3434
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-84 kcal/mol
Surface area26680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-159 kcal/mol
Surface area51720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.780, 133.780, 161.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 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 / CD11 antigen-like family member A


Mass: 20554.525 Da / Num. of mol.: 2 / Fragment: UNP residues 153-332 / Mutation: L186C, F324C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD11A, ITGAL, LFA-1 / Plasmid: PET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701

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Antibody , 2 types, 4 molecules HXLY

#2: Antibody Heavy chain of Fab fragment of AL-57 against alpha L I domain


Mass: 23765.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody light chain of Fab fragment of AL-57 against alpha L I domain


Mass: 23016.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 708 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M (NH4)2SO4, 0.1M NaAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793688 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793688 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 70437 / % possible obs: 97.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 / Χ2: 1.151 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.354.90.47437861.03178.8
2.35-2.415.30.4842471.03289.6
2.41-2.486.10.45347181.03198.4
2.48-2.557.30.43247891.03399.9
2.55-2.637.80.36447831.047100
2.63-2.7380.29948101.082100
2.73-2.8480.23447891.092100
2.84-2.9780.16448011.096100
2.97-3.1280.12347951.107100
3.12-3.3280.08948031.171100
3.32-3.577.90.07247801.301100
3.57-3.937.90.07448241.37100
3.93-4.57.70.06147921.362100
4.5-5.677.60.04748341.238100
5.67-507.80.03448861.11899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.537 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3449 5.1 %RANDOM
Rwork0.17 ---
obs0.173 67977 94.48 %-
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: 18.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9365 0 32 700 10097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229612
X-RAY DIFFRACTIONr_bond_other_d0.0010.026422
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.95313048
X-RAY DIFFRACTIONr_angle_other_deg0.8073.00315697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46351203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83424.529393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.058151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291532
X-RAY DIFFRACTIONr_chiral_restr0.0660.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021932
X-RAY DIFFRACTIONr_mcbond_it1.10836014
X-RAY DIFFRACTIONr_mcbond_other0.20832445
X-RAY DIFFRACTIONr_mcangle_it1.8459723
X-RAY DIFFRACTIONr_scbond_it1.29233598
X-RAY DIFFRACTIONr_scangle_it1.94853324
LS refinement shellResolution: 2.3→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 103 -
Rwork0.215 1716 -
all-1819 -
obs--34.5 %
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)
15.15841.11143.55192.36982.36975.3379-0.165-0.35250.20090.0650.05530.0679-0.3449-0.32190.10960.09750.07260.0070.12240.00640.045449.741-32.16114.407
23.64592.45784.14233.95692.48496.5147-0.1329-0.30770.14330.1672-0.0391-0.1716-0.1720.21480.17210.08290.0596-0.05180.1877-0.0080.108257.787-35.62115.356
36.9078-1.7292.43634.78260.66811.2424-0.1953-0.27790.52820.09780.1819-0.1383-0.41170.1890.01350.0902-0.0128-0.03560.1194-0.03240.13961.581-27.90112.983
42.4444-0.53410.57782.01750.17414.0659-0.2264-0.1979-0.18410.13940.1336-0.13860.30210.27430.09290.13420.1080.02160.15330.03390.141754.811-43.8714.812
54.2204-2.11-0.91163.98651.0915.1362-0.1357-0.2963-0.2136-0.04140.13810.0243-0.0385-0.5471-0.00250.16560.10440.05660.22490.08160.087941.914-42.84620.641
69.986-7.71811.109763.9642-5.93812.78820.0358-1.1744-0.17210.0052-0.3265-0.6867-0.13910.91070.29080.31230.2950.04950.41750.05870.10652.429-39.24731.289
74.241.0786-2.2122.2716-1.48713.43220.2745-0.1850.07080.2001-0.14280.26530.0197-0.0668-0.13160.1392-0.0657-0.02290.1012-0.02540.13328.916-83.54215.616
810.16586.7046-7.972413.7777-7.570212.97350.07660.00290.05180.0130.20590.6750.9843-0.2827-0.28260.1682-0.0357-0.06310.1206-0.02190.27294.451-91.36311.937
93.29690.3853-1.10714.25210.19023.50830.3108-0.16280.380.2977-0.25130.5362-0.3063-0.0328-0.05950.1336-0.06230.06960.0568-0.05090.218210.542-72.77414.838
109.0211.8764-6.99681.8784.445528.83090.4147-0.98640.46430.01670.5292-0.554-1.05812.1401-0.94390.3363-0.16460.09790.2451-0.09040.382121.387-66.39218.523
115.3879-4.01692.620410.1601-5.45892.98920.1688-0.25960.22821.0636-0.1093-0.6112-0.20680.5709-0.05950.2612-0.15780.03410.2332-0.04660.188320.379-77.13825.348
124.6707-5.4527-2.557726.13383.12781.4016-0.1635-0.37370.06580.75270.2151-0.39940.2695-0.2339-0.05160.2571-0.0184-0.09290.4378-0.06550.082912.772-79.7731.426
134.2311-0.75183.58792.4803-1.42386.61840.39580.0414-0.9622-0.2813-0.03230.18210.6092-0.4443-0.36360.1352-0.13420.03370.28-0.09130.18722.613-51.423-12.187
145.2925-0.2540.45683.06550.10323.7998-0.1267-0.0289-0.03830.199-0.06450.10650.051-0.430.19130.093-0.06390.07040.2354-0.08740.116326.659-44.684-3.778
155.07740.96872.5530.25460.71563.2225-0.16550.26350.1010.0475-0.01290.0819-0.0764-0.4740.17850.0848-0.0230.06180.2977-0.06890.133525.24-42.706-10.194
160.4530.35470.75780.99930.23031.45040.0509-0.03070.0231-0.0447-0.0320.04940.2645-0.1809-0.0190.0928-0.01960.05920.3941-0.06210.217524.327-46.565-25.322
171.7652-0.3009-0.18861.91610.83764.44710.0982-0.30670.1729-0.16070.0128-0.1517-0.15450.2688-0.1110.0593-0.0789-0.00820.1909-0.03350.163223.66-49.748-42.162
186.14470.0637-8.51213.1004-0.761517.3881-0.14320.0427-0.4028-0.2482-0.08430.21520.6368-0.74260.22740.1487-0.0619-0.05870.2153-0.00350.228918.72-57.144-41.834
193.6264-1.8545-5.18652.49375.08313.37040.13840.38590.3147-0.17190.0699-0.0131-0.9035-0.1925-0.20830.169-0.0223-0.03380.13390.07580.131943.513-28.89-19.591
203.9707-0.8151-1.12691.15681.1815.4557-0.17130.2297-0.0915-0.04270.1019-0.14920.18220.22680.06950.0537-0.03050.00230.09690.00390.046246.496-37.804-14.782
215.376-1.6407-4.27871.77281.657912.7055-0.05590.793-0.0222-0.0849-0.07990.0361-0.3496-0.72160.13570.0772-0.0657-0.01520.20360.00280.109440.187-36.088-18.099
228.43730.94541.41971.0655-0.26171.8533-0.1484-0.0728-0.1385-0.18940.08930.1788-0.1636-0.02530.05910.096-0.02980.00860.1536-0.0450.140324.401-40.814-47.886
2311.8631.42632.44290.85610.45210.8318-0.16-0.71531.3524-0.1214-0.13350.2166-0.215-0.02680.29350.1621-0.0641-0.00850.1698-0.09260.249125.117-32.227-45.827
248.34351.4481.52511.53940.19752.2287-0.13420.05860.6864-0.28720.04480.4032-0.2593-0.01970.08940.1785-0.0514-0.02940.1056-0.06420.222724.567-35.469-48.612
2519.9389-4.3967-8.31684.3372.90115.0150.42060.77680.5818-0.1747-0.2045-0.4419-0.42680.5888-0.2161-0.0087-0.1391-0.02040.46320.11310.169144.019-70.093-10.792
264.15851.2462-0.23212.01960.40634.05650.10680.1094-0.16710.2637-0.1032-0.28430.09810.6641-0.0037-0.0338-0.0434-0.07230.24170.070.125940.417-75.989-3.155
274.79232.252-3.63911.4682-1.59775.23720.02160.39080.0830.1941-0.0071-0.22730.02220.4473-0.0144-0.0657-0.0186-0.0720.24430.04380.082736.97-75.438-9.864
2815.0694-4.611511.99151.5541-4.555517.37540.0540.9310.3234-0.1907-0.327-0.2758-0.32060.92670.27290.08430.09030.03350.31410.06460.161641.582-70.615-49.108
293.7278-2.23322.48642.798-2.59995.19210.0614-0.2106-0.03270.1328-0.0725-0.4492-0.33020.41150.011-0.06520.02810.04260.26520.0060.057841.946-71.257-38.449
307.25370.97264.936812.2488-3.449818.4834-0.66430.27241.0251.0179-0.5244-1.3657-2.64641.25821.1888-0.0421-0.04460.02210.23890.05570.191848.485-64.975-36.751
313.0079-1.74563.69833.2887-4.824412.64540.26270.2771-0.3117-0.2329-0.0527-0.08391.03830.0755-0.21010.15950.0366-0.01440.1663-0.07570.18421.112-91.492-19.061
323.4241-0.66552.12120.6513-0.4026.00810.0310.3513-0.12-0.08620.0519-0.00330.034-0.0315-0.0830.0503-0.0164-0.00290.12450.02250.096119.577-83.408-12.639
332.9660.36732.25061.7642-1.920514.4013-0.08390.5548-0.0412-0.04060.0034-0.14690.43030.76590.08040.02660.03140.0190.1948-0.01120.141126.576-85.804-14.4
345.46390.7706-2.10923.08420.13184.1080.21640.3724-0.1112-0.2122-0.0695-0.5640.03790.4073-0.14690.06260.10150.0270.42090.05620.093538.864-80.394-45.276
3516.953.5067-3.27413.0237-2.03361.4328-0.50290.0328-1.7476-0.31180.0189-0.7910.8280.49920.48410.22720.19870.13360.506-0.05870.476442.316-91.596-46.302
3626.8122-2.7937-7.98812.05840.94668.53580.08890.0775-0.6799-0.221-0.0594-0.49720.22760.3132-0.02960.14610.12230.02010.4110.00910.213840.8-82.541-41.787
3712.94964.58920.08794.0599-0.97553.5803-0.51090.5908-0.6853-0.84580.4014-0.6720.94061.15470.10960.54230.22750.21570.7761-0.14210.353739.387-87.546-53.488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A128 - 160
2X-RAY DIFFRACTION2A161 - 179
3X-RAY DIFFRACTION3A180 - 200
4X-RAY DIFFRACTION4A201 - 263
5X-RAY DIFFRACTION5A264 - 297
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