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- PDB-4llq: Structure of redesigned IgG1 first constant and lambda domains (C... -

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Basic information

Entry
Database: PDB / ID: 4llq
TitleStructure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant redesign 2 beta, CRD2b) at 1.42A
Components
  • mutated CH1
  • mutated light chain Clambda
KeywordsIMMUNE SYSTEM / IgG domain redesign
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / 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 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / 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 / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / extracellular region / membrane / 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 C1-set / Immunoglobulin C1-set domain ...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
Chem-PG6 / Immunoglobulin heavy constant gamma 1 / Immunoglobulin lambda constant 3 / Uncharacterized protein DKFZp686G11190 / IGL@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mutated CH1
B: mutated light chain Clambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9623
Polymers27,6962
Non-polymers2661
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-10 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.742, 62.585, 71.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mutated CH1


Mass: 11671.084 Da / Num. of mol.: 1 / Mutation: F198G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686G11190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MZQ6, UniProt: P01857*PLUS
#2: Antibody mutated light chain Clambda


Mass: 16024.999 Da / Num. of mol.: 1 / Mutation: L61A, S101W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PJR7, UniProt: P0DOY3*PLUS
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 1.72 Å3/Da / Density % sol: 28.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 39% PEG 6K + 5mM tri Sodium Citrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→47.011 Å / Num. all: 36179 / Num. obs: 36179 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.42→1.5 Å / Rmerge(I) obs: 0.527 / Rsym value: 0.527 / % possible all: 98.6

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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 4LLD

4lld


Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 0.998 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22084 1805 5 %RANDOM
Rwork0.18767 ---
all0.189 36178 --
obs0.18929 34368 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: 16.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.42→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 10 203 1663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221517
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9622083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93625.11643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.039151
X-RAY DIFFRACTIONr_chiral_restr0.0740.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221101
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_it1.41931010
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49551653
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5178507
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.35411430
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: 1.424→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 106 -
Rwork0.263 2495 -
obs--100 %

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