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- PDB-3o11: Anti-beta-amyloid antibody c706 fab in space group c2 -

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Basic information

Entry
Database: PDB / ID: 3o11
TitleAnti-beta-amyloid antibody c706 fab in space group c2
Components
  • C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera
  • C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / 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 / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / 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 / Interleukin-4 and Interleukin-13 signaling / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: J.Mol.Recognit. / Year: 2011
Title: His-tag binding by antibody C706 mimics beta-amyloid recognition.
Authors: Teplyakov, A. / Obmolova, G. / Canziani, G. / Zhao, Y. / Gutshall, L. / Jung, S.S. / Gilliland, G.L.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Jul 26, 2023Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 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
L: C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera
H: C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera
A: C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera
B: C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera


Theoretical massNumber of molelcules
Total (without water)94,5174
Polymers94,5174
Non-polymers00
Water1,72996
1
L: C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera
H: C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera


Theoretical massNumber of molelcules
Total (without water)47,2592
Polymers47,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area20480 Å2
MethodPISA
2
A: C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera
B: C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera


Theoretical massNumber of molelcules
Total (without water)47,2592
Polymers47,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.040, 45.020, 158.200
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody C706 LIGHT CHAIN variable region, Ig kappa chain C region chimera


Mass: 23057.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: IGKC / Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P01834
#2: Antibody C706 HEAVY CHAIN variable region, Ig gamma-1 chain C region chimera


Mass: 24200.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: IGHG1 / Cell (production host): HUMAN EMBRYONIC KIDNEY (HEK) CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P01857
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / pH: 3.5
Details: 0.1 M CITRATE PH 3.5, 18% PEG 8000 CRYO CONDITIONS, 0.1 M CITRATE PH 3.5, 25% PEG 8000, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→53 Å / Num. obs: 20634 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 96 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.4 / % possible all: 82.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MCL

3mcl


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.849 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.543 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.304 432 2.1 %RANDOM
Rwork0.22 ---
obs0.223 20043 83.3 %-
all-20043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å2-0.49 Å2
2--3.55 Å20 Å2
3----1.05 Å2
Refine analyzeLuzzati coordinate error free: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 0 96 6636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.949148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63124.348253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.009151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8691520
X-RAY DIFFRACTIONr_chiral_restr0.0830.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025044
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22855
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.85324389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.32766974
X-RAY DIFFRACTIONr_scbond_it17.315122663
X-RAY DIFFRACTIONr_scangle_it24.593992174
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.82 37 -
Rwork0.454 1389 -
obs--82.3 %

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