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- PDB-4irz: Crystal structure of A4b7 headpiece complexed with Fab Natalizumab -

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Basic information

Entry
Database: PDB / ID: 4irz
TitleCrystal structure of A4b7 headpiece complexed with Fab Natalizumab
Components
  • (Fab Natalizumab ...) x 2
  • Integrin alpha4 subunit
KeywordsIMMUNE SYSTEM / rolling and firm adhesion / MAdCAM
Function / homology
Function and homology information


cell-matrix adhesion involved in ameboidal cell migration / C-X3-C chemokine binding / integrin alpha4-beta7 complex / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / leukocyte tethering or rolling / positive regulation of vascular endothelial cell proliferation / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / receptor clustering ...cell-matrix adhesion involved in ameboidal cell migration / C-X3-C chemokine binding / integrin alpha4-beta7 complex / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / leukocyte tethering or rolling / positive regulation of vascular endothelial cell proliferation / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / receptor clustering / endodermal cell differentiation / positive regulation of endothelial cell apoptotic process / substrate adhesion-dependent cell spreading / integrin-mediated signaling pathway / cellular response to amyloid-beta / integrin binding / external side of plasma membrane / metal ion binding
Similarity search - Function
Integrin domains. Chain A, domain 2 / Integrin alpha, N-terminal / : / Integrin alpha Ig-like domain 3 / 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 domains. Chain A, domain 2 / Integrin alpha, N-terminal / : / Integrin alpha Ig-like domain 3 / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / DI(HYDROXYETHYL)ETHER / Integrin subunit alpha 4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsYu, Y. / Schurpf, T. / Springer, T.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: How natalizumab binds and antagonizes alpha 4 integrins.
Authors: Yu, Y. / Schurpf, T. / Springer, T.A.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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 / _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_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha4 subunit
L: Fab Natalizumab light chain
H: Fab Natalizumab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,85214
Polymers112,9363
Non-polymers1,91611
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-13 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.610, 77.890, 217.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Integrin alpha4 subunit


Mass: 65644.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): CHO Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: G1TY34*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody Fab Natalizumab light chain


Mass: 23289.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: humanized antibody / Source: (gene. exp.) Homo sapiens (human) / Description: humanized antibody
#3: Antibody Fab Natalizumab heavy chain


Mass: 24001.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: humanized antibody / Source: (gene. exp.) Homo sapiens (human) / Description: humanized antibody

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Sugars , 2 types, 5 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 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 , 5 types, 19 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3S
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 6%PEG2000,0.1M Bicine pH9.0, 5%dioxane, 300mM NDSB-195, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011
RadiationMonochromator: double silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→12.7 Å / Num. all: 30383 / Num. obs: 30297 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→44.619 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 1537 5.07 %
Rwork0.2367 --
obs0.2392 30290 99.72 %
all-30290 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→44.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 118 13 7968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058214
X-RAY DIFFRACTIONf_angle_d0.611175
X-RAY DIFFRACTIONf_dihedral_angle_d12.3533008
X-RAY DIFFRACTIONf_chiral_restr0.0381227
X-RAY DIFFRACTIONf_plane_restr0.0021432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8404-2.93210.45161470.39672502X-RAY DIFFRACTION97
2.9321-3.03680.4451190.35912580X-RAY DIFFRACTION100
3.0368-3.15840.36221420.33072583X-RAY DIFFRACTION100
3.1584-3.30210.3761220.30682590X-RAY DIFFRACTION100
3.3021-3.47610.36641340.27052593X-RAY DIFFRACTION100
3.4761-3.69380.29191310.2572627X-RAY DIFFRACTION100
3.6938-3.97890.25641430.23792580X-RAY DIFFRACTION100
3.9789-4.37890.25161510.19842609X-RAY DIFFRACTION100
4.3789-5.01190.21481390.17042626X-RAY DIFFRACTION100
5.0119-6.31160.25471540.19072666X-RAY DIFFRACTION100
6.3116-44.6240.24541550.20282797X-RAY DIFFRACTION100
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)
13.26921.263-0.61194.2239-1.95783.6088-0.11910.1234-0.1121-0.15890.151-0.17840.27010.4976-0.0520.17810.0569-0.00680.3152-0.04770.34939.519-25.723686.3934
21.3624-0.6689-0.39352.50381.09683.6745-0.04170.08410.0458-0.17870.01040.1766-0.33080.02010.04050.2527-0.02880.00190.28530.03390.2648-2.8099-11.433782.1848
32.5789-0.91351.58713.7184-3.36568.88970.36290.42010.1194-0.4084-0.08640.0524-0.33240.4487-0.21860.60730.10170.11680.3865-0.06250.442219.9846-2.383837.3583
41.7757-0.84290.41566.9505-7.23769.03060.2162-0.03770.1497-0.3706-0.3249-0.05690.33950.61490.02610.4438-0.00040.10610.4796-0.08290.353119.3071-4.395344.0978
53.20760.289-0.40144.02290.53731.8021-0.07830.33570.1895-0.00640.0794-0.4521-0.44620.1244-0.08040.5706-0.1646-0.16390.22710.02190.24784.94918.1155125.0245
66.70121.1619-1.62943.07550.85925.5484-0.19650.08320.3646-0.15970.0855-0.2522-0.56690.85190.10760.3205-0.13270.00310.48790.07650.34783.63229.7559113.4144
71.5205-0.15230.39962.45191.09252.8335-0.2379-0.44590.33660.0004-0.15070.1868-0.4330.03660.29790.2986-0.04620.00510.32580.02210.3496-1.454910.2095124.987
88.25773.2902-3.84969.1516-3.36646.58490.0734-0.86470.45330.3594-0.08390.1499-0.2469-0.54960.10410.45260.0042-0.0990.6002-0.05890.2968-6.89139.5478143.7358
93.61730.31981.29294.58070.46485.09620.2863-0.7975-0.83790.87480.19740.14440.7252-0.8878-0.29750.49370.1377-0.0830.93980.25430.5644-3.65720.9776149.1394
104.4692-1.2761-3.30223.65810.54782.72920.64470.29430.9634-0.995-0.08590.146-0.6899-0.3706-0.62050.48380.00020.01530.3984-0.04430.5058-22.548913.7303112.5106
113.3694-0.4106-0.85451.51281.07354.9412-0.09090.03780.1708-0.1016-0.01390.1105-0.3907-0.37780.07170.27640.03850.00190.1586-0.03080.365-17.09036.0674113.4937
121.63820.6791.54221.27061.10162.5848-0.0244-1.2190.6840.4432-0.1254-0.01250.4653-0.3430.23890.55530.182-0.01241.0223-0.24980.5775-17.506212.928144.9755
131.45751.0752-0.44283.57513.32494.9802-0.2709-0.61310.50460.34850.21540.1786-0.02110.12060.05780.61120.4333-0.07950.9599-0.31530.6657-18.785617.8922146.2278
141.03050.9742.35632.11661.3727.1903-0.1491-0.06880.47590.637-0.10910.2888-0.3818-0.49170.1710.91980.1514-0.05781.1936-0.44070.6901-18.803919.1369158.181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:81
2X-RAY DIFFRACTION2chain A and resid 82:430
3X-RAY DIFFRACTION3chain A and resid 431:515
4X-RAY DIFFRACTION4chain A and resid 516:592
5X-RAY DIFFRACTION5chain H and resid 1:16
6X-RAY DIFFRACTION6chain H and resid 17:81
7X-RAY DIFFRACTION7chain H and resid 82:138
8X-RAY DIFFRACTION8chain H and resid 144:193
9X-RAY DIFFRACTION9chain H and resid 194:222
10X-RAY DIFFRACTION10chain L and resid 3:30
11X-RAY DIFFRACTION11chain L and resid 31:98
12X-RAY DIFFRACTION12chain L and resid 99:141
13X-RAY DIFFRACTION13chain L and resid 142:179
14X-RAY DIFFRACTION14chain L and resid 180:210

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