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- PDB-4llu: Structure of Pertuzumab Fab with light chain Clambda at 2.16A -

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Basic information

Entry
Database: PDB / ID: 4llu
TitleStructure of Pertuzumab Fab with light chain Clambda at 2.16A
Components
  • Light chain CLAMBDA
  • PERTUZUMAB FAB Heavy chain
KeywordsIMMUNE SYSTEM / Fab
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin mediated immune response / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Immunoglobulin lambda constant 3 / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPustilnik, A. / Lewis, S.M. / Wu, X. / Sereno, A. / Huang, F. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. ...Pustilnik, A. / Lewis, S.M. / Wu, X. / Sereno, A. / Huang, F. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / Kuhlman, B. / Demarest, S.J. / Atwell, S.
CitationJournal: Nat.Biotechnol. / Year: 2014
Title: Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface.
Authors: Lewis, S.M. / Wu, X. / Pustilnik, A. / Sereno, A. / Huang, F. / Rick, H.L. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / ...Authors: Lewis, S.M. / Wu, X. / Pustilnik, A. / Sereno, A. / Huang, F. / Rick, H.L. / Guntas, G. / Leaver-Fay, A. / Smith, E.M. / Ho, C. / Hansen-Estruch, C. / Chamberlain, A.K. / Truhlar, S.M. / Conner, E.M. / Atwell, S. / Kuhlman, B. / Demarest, S.J.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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
A: PERTUZUMAB FAB Heavy chain
B: Light chain CLAMBDA
C: PERTUZUMAB FAB Heavy chain
D: Light chain CLAMBDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8418
Polymers94,4934
Non-polymers3474
Water4,414245
1
A: PERTUZUMAB FAB Heavy chain
B: Light chain CLAMBDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4024
Polymers47,2472
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-49 kcal/mol
Surface area19260 Å2
MethodPISA
2
C: PERTUZUMAB FAB Heavy chain
D: Light chain CLAMBDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4394
Polymers47,2472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-32 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.024, 69.739, 70.828
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PERTUZUMAB FAB Heavy chain


Mass: 24259.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: S6C4R2*PLUS
#2: Antibody Light chain CLAMBDA


Mass: 22987.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: P0DOY3*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM Sodium Acetate pH 4.5 + 10% MPD + 30% PEG 2000 MME + 200mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 7, 2012
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.16→19.902 Å / Num. all: 52049 / Num. obs: 52049 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.175
Reflection shellResolution: 2.16→2.28 Å / Rmerge(I) obs: 0.67 / % possible all: 94.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S78

1s78


Resolution: 2.16→19.9 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.865 / SU B: 6.206 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27279 2654 5.1 %RANDOM
Rwork0.22241 ---
all0.225 52049 --
obs0.22501 49395 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.981 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-0.21 Å2
2--0.25 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.16→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 0 19 245 6702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9569057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88724.274248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3691521
X-RAY DIFFRACTIONr_chiral_restr0.0830.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215023
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65534267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04556898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.03282364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.356112159
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 174 -
Rwork0.303 3483 -
obs--100 %

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