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- PDB-6fg1: CRYSTAL STRUCTURE OF FAB OF NATALIZUMAB IN COMPLEX WITH FAB OF NAA32. -

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Basic information

Entry
Database: PDB / ID: 6fg1
TitleCRYSTAL STRUCTURE OF FAB OF NATALIZUMAB IN COMPLEX WITH FAB OF NAA32.
Components
  • (HEAVY CHAIN OF FAB ...) x 2
  • (LIGHT CHAIN OF FAB ...) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBertrand, T. / Pouzieux, S.
CitationJournal: Nat. Med. / Year: 2019
Title: A single T cell epitope drives the neutralizing anti-drug antibody response to natalizumab in multiple sclerosis patients.
Authors: Cassotta, A. / Mikol, V. / Bertrand, T. / Pouzieux, S. / Le Parc, J. / Ferrari, P. / Dumas, J. / Auer, M. / Deisenhammer, F. / Gastaldi, M. / Franciotta, D. / Silacci-Fregni, C. / Fernandez ...Authors: Cassotta, A. / Mikol, V. / Bertrand, T. / Pouzieux, S. / Le Parc, J. / Ferrari, P. / Dumas, J. / Auer, M. / Deisenhammer, F. / Gastaldi, M. / Franciotta, D. / Silacci-Fregni, C. / Fernandez Rodriguez, B. / Giacchetto-Sasselli, I. / Foglierini, M. / Jarrossay, D. / Geiger, R. / Sallusto, F. / Lanzavecchia, A. / Piccoli, L.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAVY CHAIN OF FAB NAA32
D: LIGHT CHAIN OF FAB NAA32
H: HEAVY CHAIN OF FAB NATALIZUMAB
L: LIGHT CHAIN OF FAB NATALIZUMAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7797
Polymers98,5034
Non-polymers2763
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-59 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.101, 189.101, 87.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Antibody , 4 types, 4 molecules ADHL

#1: Antibody HEAVY CHAIN OF FAB NAA32


Mass: 26127.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody LIGHT CHAIN OF FAB NAA32


Mass: 23368.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody HEAVY CHAIN OF FAB NATALIZUMAB


Mass: 25427.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody LIGHT CHAIN OF FAB NATALIZUMAB


Mass: 23579.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 256 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 4.04 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: Na2 Malonate 1.7M - pH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.03→87.6 Å / Num. obs: 81847 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 37.63 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.9
Reflection shellResolution: 2.03→2.07 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRZ, 4NM4 and 3X3F

4irz

4nm4

3x3f


Resolution: 2.03→87.26 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.865 / SU R Cruickshank DPI: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3195 5.03 %RANDOM
Rwork0.266 ---
obs0.267 63528 59.6 %-
Displacement parametersBiso mean: 39.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.7191 Å20 Å20 Å2
2--0.7191 Å20 Å2
3----1.4382 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.03→87.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 18 253 6985
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086905HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089399HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2283SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1144HARMONIC5
X-RAY DIFFRACTIONt_it6905HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion915SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7630SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2538 -6.79 %
Rwork0.2489 343 -
all0.2492 368 -
obs--4.63 %

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