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- PDB-6fg2: CRYSTAL STRUCTURE OF FAB OF NATALIZUMAB IN COMPLEX WITH FAB OF NAA84. -

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Basic information

Entry
Database: PDB / ID: 6fg2
TitleCRYSTAL STRUCTURE OF FAB OF NATALIZUMAB IN COMPLEX WITH FAB OF NAA84.
Components
  • HEAVY CHAIN FAB NAA84
  • HEAVY CHAIN FAB NATALIZUMAB
  • LIGHT CHAIN FAB NAA84
  • LIGHT CHAIN FAB NATALIZUMAB
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: 2.788 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: 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
D: HEAVY CHAIN FAB NAA84
E: LIGHT CHAIN FAB NAA84
F: HEAVY CHAIN FAB NAA84
G: LIGHT CHAIN FAB NAA84
H: HEAVY CHAIN FAB NATALIZUMAB
I: HEAVY CHAIN FAB NATALIZUMAB
L: LIGHT CHAIN FAB NATALIZUMAB
M: LIGHT CHAIN FAB NATALIZUMAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,4459
Polymers195,0218
Non-polymers4241
Water00
1
D: HEAVY CHAIN FAB NAA84
E: LIGHT CHAIN FAB NAA84
I: HEAVY CHAIN FAB NATALIZUMAB
M: LIGHT CHAIN FAB NATALIZUMAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9355
Polymers97,5104
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: HEAVY CHAIN FAB NAA84
G: LIGHT CHAIN FAB NAA84
H: HEAVY CHAIN FAB NATALIZUMAB
L: LIGHT CHAIN FAB NATALIZUMAB


Theoretical massNumber of molelcules
Total (without water)97,5104
Polymers97,5104
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.404, 66.619, 199.502
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HEAVY CHAIN FAB NAA84


Mass: 25857.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody LIGHT CHAIN FAB NAA84


Mass: 22878.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody HEAVY CHAIN FAB NATALIZUMAB


Mass: 25427.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody LIGHT CHAIN FAB NATALIZUMAB


Mass: 23346.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: 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
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: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: MES 100mM - PEG 400 35% - NaCl 200mM - MPD 4% - 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: 2.788→197.06 Å / Num. obs: 40020 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 69.53 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.3
Reflection shellResolution: 2.788→3.143 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, 3S37 and 4OD2

4irz

3s37

4od2


Resolution: 2.788→55.21 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.834 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.485
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1992 4.98 %RANDOM
Rwork0.238 ---
obs0.239 40000 58.6 %-
Displacement parametersBiso mean: 56.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.2469 Å20 Å23.3592 Å2
2---7.5403 Å20 Å2
3---5.2935 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.788→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13096 0 28 0 13124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00713457HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0318346HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4408SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2245HARMONIC5
X-RAY DIFFRACTIONt_it13457HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1789SEMIHARMONIC5
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_contact14256SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5588 -5 %
Rwork0.4465 --
all0.4522 100 -
obs--2.01 %

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