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- PDB-1mhp: Crystal structure of a chimeric alpha1 integrin I-domain in compl... -

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Basic information

Entry
Database: PDB / ID: 1mhp
TitleCrystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody
Components
  • FAB FRAGMENT, light chain
  • Fab fragment, heavy chain
  • integrin alpha 1, (RESIDUES 169-360)
KeywordsIMMUNE SYSTEM / integrin / cell adhesion / receptor / antibody
Function / homology
Function and homology information


Integrin cell surface interactions / Smooth Muscle Contraction / integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / phosphatase activator activity / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway ...Integrin cell surface interactions / Smooth Muscle Contraction / integrin alpha1-beta1 complex / cellular extravasation / collagen binding involved in cell-matrix adhesion / phosphatase activator activity / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / collagen binding / neuron projection morphogenesis / neutrophil chemotaxis / acrosomal vesicle / cell-matrix adhesion / integrin-mediated signaling pathway / cell chemotaxis / cell-cell adhesion / vasodilation / integrin binding / positive regulation of neuron apoptotic process / protein phosphatase binding / perikaryon / cell adhesion / positive regulation of MAPK cascade / signaling receptor binding / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / cell surface / metal ion binding
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : ...: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKarpusas, M. / Taylor, F. / Ferrant, J. / Weinreb, P. / Garber, E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the alpha 1 beta 1 Integrin I Domain in Complex with an Antibody Fab Fragment
Authors: Karpusas, M. / Ferrant, J. / Weinreb, P. / Carmillo, A. / Taylor, F. / Garber, E.
History
DepositionAug 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_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 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING FOR ...SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING FOR CHAINS H AND X (Fab fragment, heavy chain) AND FOR CHAINS L AND Y (FAB FRAGMENT, light chain).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: integrin alpha 1, (RESIDUES 169-360)
H: Fab fragment, heavy chain
L: FAB FRAGMENT, light chain
B: integrin alpha 1, (RESIDUES 169-360)
X: Fab fragment, heavy chain
Y: FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0568
Polymers135,9466
Non-polymers1102
Water00
1
A: integrin alpha 1, (RESIDUES 169-360)
H: Fab fragment, heavy chain
L: FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0284
Polymers67,9733
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-36 kcal/mol
Surface area25660 Å2
MethodPISA
2
B: integrin alpha 1, (RESIDUES 169-360)
X: Fab fragment, heavy chain
Y: FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0284
Polymers67,9733
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-24 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.09, 255.09, 38.64
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein integrin alpha 1, (RESIDUES 169-360) / Laminin and collagen receptor / VLA-1 / CD49a


Mass: 21629.518 Da / Num. of mol.: 2 / Fragment: alpha1 I-domain / Mutation: G217V, R218Q, Q219R, L222R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P18614
#2: Antibody Fab fragment, heavy chain


Mass: 23141.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody FAB FRAGMENT, light chain


Mass: 23201.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 1500, Tris, NaCl, beta-mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
220 mMTris1droppH7.4
3150 mM1dropNaCl
41 mM1dropMnCl2
55 mMbeta-mercaptoethanol1drop
620-30 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. all: 36501 / Num. obs: 35275 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.92
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.29 / % possible all: 87.7
Reflection
*PLUS
Lowest resolution: 500 Å
Reflection shell
*PLUS
% possible obs: 87.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 2423 RANDOM
Rwork0.213 --
all0.239 36501 -
obs0.222 35259 -
Refinement stepCycle: LAST / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7941 0 2 0 7943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007396
X-RAY DIFFRACTIONc_angle_deg1.43251
Refinement
*PLUS
Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.43

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