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- PDB-8ecq: Bovine Fab 2G3 -

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Basic information

Entry
Database: PDB / ID: 8ecq
TitleBovine Fab 2G3
Components
  • 2G3 Fab Heavy chain
  • 2G3 Fab Light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis ...CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / 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 / blood microparticle / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoglobulin lambda constant 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2.
Authors: Huang, R. / Warner Jenkins, G. / Kim, Y. / Stanfield, R.L. / Singh, A. / Martinez-Yamout, M. / Kroon, G.J. / Torres, J.L. / Jackson, A.M. / Kelley, A. / Shaabani, N. / Zeng, B. / Bacica, M. ...Authors: Huang, R. / Warner Jenkins, G. / Kim, Y. / Stanfield, R.L. / Singh, A. / Martinez-Yamout, M. / Kroon, G.J. / Torres, J.L. / Jackson, A.M. / Kelley, A. / Shaabani, N. / Zeng, B. / Bacica, M. / Chen, W. / Warner, C. / Radoicic, J. / Joh, J. / Dinali Perera, K. / Sang, H. / Kim, T. / Yao, J. / Zhao, F. / Sok, D. / Burton, D.R. / Allen, J. / Harriman, W. / Mwangi, W. / Chung, D. / Teijaro, J.R. / Ward, A.B. / Dyson, H.J. / Wright, P.E. / Wilson, I.A. / Chang, K.O. / McGregor, D. / Smider, V.V.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 2G3 Fab Light chain
H: 2G3 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2436
Polymers50,7712
Non-polymers4724
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-25 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.373, 66.373, 232.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11H-407-

HOH

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Components

#1: Antibody 2G3 Fab Light chain


Mass: 22527.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: P0DOY2
#2: Antibody 2G3 Fab Heavy chain


Mass: 28243.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% glycerol, 0.1M Mes, 5% Peg1000, 30% Peg600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2→46.93 Å / Num. obs: 36241 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.5 % / Biso Wilson estimate: 36.18 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.017 / Rrim(I) all: 0.077 / Χ2: 1.031 / Net I/av σ(I): 29.6 / Net I/σ(I): 29.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1611 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.411 / Rrim(I) all: 0.911 / Χ2: 1.177 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6oo0

6oo0


Resolution: 2→46.93 Å / SU ML: 0.2374 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 1795 4.97 %
Rwork0.2141 34339 -
obs0.2161 36134 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.45 Å2
Refinement stepCycle: LAST / Resolution: 2→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 30 130 3695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753645
X-RAY DIFFRACTIONf_angle_d0.76494965
X-RAY DIFFRACTIONf_chiral_restr0.0484573
X-RAY DIFFRACTIONf_plane_restr0.0055633
X-RAY DIFFRACTIONf_dihedral_angle_d12.78371291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37981000.35732380X-RAY DIFFRACTION91.18
2.05-2.110.38691380.31942547X-RAY DIFFRACTION98.06
2.11-2.180.27351340.28962596X-RAY DIFFRACTION99.06
2.18-2.260.31861350.27122610X-RAY DIFFRACTION99.89
2.26-2.350.25651380.25422627X-RAY DIFFRACTION100
2.35-2.450.29381220.23912645X-RAY DIFFRACTION100
2.45-2.580.26631560.23852609X-RAY DIFFRACTION100
2.58-2.750.31041490.23622635X-RAY DIFFRACTION100
2.75-2.960.29011210.23022672X-RAY DIFFRACTION100
2.96-3.260.27671370.21942675X-RAY DIFFRACTION100
3.26-3.730.26111320.20562715X-RAY DIFFRACTION99.93
3.73-4.690.18931600.16982729X-RAY DIFFRACTION100
4.69-46.930.22641730.18422899X-RAY DIFFRACTION99.93

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