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- PDB-8ecz: Bovine Fab 4C1 -

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Basic information

Entry
Database: PDB / ID: 8ecz
TitleBovine Fab 4C1
Components
  • 4C1 Fab heavy chain
  • 4C1 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: 2.82 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: 4C1 Fab light chain
H: 4C1 Fab heavy chain
A: 4C1 Fab light chain
B: 4C1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3839
Polymers102,9084
Non-polymers4755
Water0
1
L: 4C1 Fab light chain
H: 4C1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6444
Polymers51,4542
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-37 kcal/mol
Surface area22310 Å2
MethodPISA
2
A: 4C1 Fab light chain
B: 4C1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7395
Polymers51,4542
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-42 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.058, 97.475, 70.385
Angle α, β, γ (deg.)90.000, 91.435, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "L" and resid 3 through 211)
d_1ens_2(chain "B" and (resid 2 through 112 or resid 124 through 279))
d_2ens_2(chain "H" and resid 2 through 279)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALCYSC1 - 213
d_21ens_1VALCYSA1 - 213
d_11ens_2VALSERD1 - 114
d_12ens_2TRPCYSD126 - 271
d_21ens_2VALCYSB2 - 261

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Antibody 4C1 Fab light chain


Mass: 22527.611 Da / Num. of mol.: 2
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 4C1 Fab heavy chain


Mass: 28926.240 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
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: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 50% MPD, 0.2M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.82→49.75 Å / Num. obs: 29956 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 55 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.102 / Rrim(I) all: 0.181 / Χ2: 1.291 / Net I/av σ(I): 7.2 / Net I/σ(I): 7.2
Reflection shellResolution: 2.82→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1238 / CC1/2: 0.315 / Rpim(I) all: 0.777 / Rrim(I) all: 1.28 / Χ2: 1.138 / % possible all: 79.1

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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: 2.82→49.75 Å / Cross valid method: FREE R-VALUE / σ(F): 155.74 / Phase error: 41.0901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 1644 5.49 %
Rwork0.2435 28302 -
obs0.2787 29946 91.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.41 Å2
Refinement stepCycle: LAST / Resolution: 2.82→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 25 0 7131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00487284
X-RAY DIFFRACTIONf_angle_d0.75949936
X-RAY DIFFRACTIONf_chiral_restr0.04761145
X-RAY DIFFRACTIONf_plane_restr0.00461268
X-RAY DIFFRACTIONf_dihedral_angle_d10.91232576
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2LX-RAY DIFFRACTIONTorsion NCS0.704087980568
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS1.82575927172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.910.368960.36471962X-RAY DIFFRACTION67.91
2.91-3.010.39761130.35612443X-RAY DIFFRACTION82.87
3.01-3.130.43011260.35072514X-RAY DIFFRACTION86.13
3.13-3.280.38631270.36192582X-RAY DIFFRACTION87.29
3.28-3.450.38391250.35492680X-RAY DIFFRACTION90.45
3.45-3.670.33461680.34512630X-RAY DIFFRACTION89.18
3.67-3.950.35821590.33152687X-RAY DIFFRACTION90.56
3.95-4.350.25261590.26862672X-RAY DIFFRACTION90.7
4.35-4.970.26621400.23392745X-RAY DIFFRACTION92.11
4.98-6.270.25041620.2362718X-RAY DIFFRACTION91.24
6.27-49.750.20551610.21232777X-RAY DIFFRACTION91.11

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