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- PDB-8ed1: Bovine Fab 5C1 -

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Basic information

Entry
Database: PDB / ID: 8ed1
TitleBovine Fab 5C1
Components
  • 5C1 Fab heavy chain
  • 5C1 Fab light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / Immunoglobulin gamma-1 heavy chain / Immunoglobulin lambda constant 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 5C1 Fab light chain
H: 5C1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8936
Polymers51,5222
Non-polymers3714
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-36 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.901, 197.413, 70.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody 5C1 Fab light chain


Mass: 22527.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: P0DOY2
#2: Antibody 5C1 Fab heavy chain


Mass: 28994.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, 10% glycerol, 20% Peg300, 5% Peg8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.31→37.4 Å / Num. obs: 27526 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 42.76 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.047 / Rrim(I) all: 0.159 / Χ2: 1.498 / Net I/av σ(I): 15.8 / Net I/σ(I): 15.8
Reflection shellResolution: 2.31→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8370 / CC1/2: 0.797 / Rpim(I) all: 0.318 / Rrim(I) all: 0.902 / Χ2: 1.015 / % possible all: 75.2

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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: 2.31→37.38 Å / SU ML: 0.372 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.6578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2667 1379 5.02 %
Rwork0.2348 26075 -
obs0.2364 27454 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.18 Å2
Refinement stepCycle: LAST / Resolution: 2.31→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 23 7 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193697
X-RAY DIFFRACTIONf_angle_d0.5725039
X-RAY DIFFRACTIONf_chiral_restr0.0427577
X-RAY DIFFRACTIONf_plane_restr0.0043644
X-RAY DIFFRACTIONf_dihedral_angle_d11.33591310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.390.42821290.39781937X-RAY DIFFRACTION68.57
2.39-2.480.43461080.35712267X-RAY DIFFRACTION78.43
2.48-2.60.36511210.3432366X-RAY DIFFRACTION82.27
2.6-2.730.35921330.32152499X-RAY DIFFRACTION86.72
2.73-2.90.34511300.31062649X-RAY DIFFRACTION90.32
2.9-3.130.37671400.29952643X-RAY DIFFRACTION91.88
3.13-3.440.32021410.27772884X-RAY DIFFRACTION98.95
3.44-3.940.26911540.23642914X-RAY DIFFRACTION99.68
3.94-4.960.20651530.1772949X-RAY DIFFRACTION99.9
4.96-37.380.1811700.16182967X-RAY DIFFRACTION96.88

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