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- PDB-8edf: Bovine Fab SKD in complex with Sars COV-2 receptor binding domain -

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Basic information

Entry
Database: PDB / ID: 8edf
TitleBovine Fab SKD in complex with Sars COV-2 receptor binding domain
Components
  • SKD Fab Light chain
  • SKD Fab heavy chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / antibody / SARS Cov-2
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 complex / immunoglobulin mediated immune response / 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 complex / immunoglobulin mediated immune response / 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / adaptive immune response / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / 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 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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / 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 / Spike glycoprotein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 4, 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 16, 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: SKD Fab Light chain
H: SKD Fab heavy chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8054
Polymers73,5843
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.841, 162.841, 125.171
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

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Components

#1: Antibody SKD 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) / Production host: Homo sapiens (human) / References: UniProt: P0DOY2
#2: Antibody SKD Fab heavy chain


Mass: 28454.834 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: Protein Spike protein S1


Mass: 22601.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 5.64 Å3/Da / Density % sol: 78.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.4M Lithium chloride, 10% Peg6000, 0.1M sodium citrate

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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: Jan 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.4→26.74 Å / Num. obs: 23014 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 92.12 Å2 / CC1/2: 0.726 / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.135 / Rrim(I) all: 0.318 / Net I/av σ(I): 5.8 / Net I/σ(I): 5.8
Reflection shellResolution: 3.4→3.55 Å / Redundancy: 5.1 % / Rmerge(I) obs: 2.39 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1145 / CC1/2: 0.403 / Rpim(I) all: 1.12 / Rrim(I) all: 2.65 / % possible all: 99.6

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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: 3.4→26.74 Å / SU ML: 0.559 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.1797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2994 1156 5.05 %
Rwork0.2759 21725 -
obs0.2771 22881 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.54 Å2
Refinement stepCycle: LAST / Resolution: 3.4→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 14 0 5053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245174
X-RAY DIFFRACTIONf_angle_d0.64147057
X-RAY DIFFRACTIONf_chiral_restr0.0449799
X-RAY DIFFRACTIONf_plane_restr0.0044911
X-RAY DIFFRACTIONf_dihedral_angle_d11.74141825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.550.43641390.41352673X-RAY DIFFRACTION96.73
3.55-3.740.39341490.38142717X-RAY DIFFRACTION97.95
3.74-3.970.41551450.35652719X-RAY DIFFRACTION98.02
3.97-4.270.34911480.31462736X-RAY DIFFRACTION98.4
4.27-4.70.28561360.2582621X-RAY DIFFRACTION94.26
4.7-5.380.25411520.24172716X-RAY DIFFRACTION96.47
5.38-6.760.27391440.26572786X-RAY DIFFRACTION97.25
6.76-26.740.22931430.20692757X-RAY DIFFRACTION92.09
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09881195508560.140276404521-0.06260762359010.5054653567030.001134772944810.183980810363-0.2967144132730.690652043959-0.217436659083-0.3549450158-0.5414171377680.161546522510.464765518177-0.311420676802-1.37038248655E-51.174720954210.394608417407-0.03611727433871.44086644019-0.3027805617231.2337975528138.501518971126.40172586418.4047447881
20.494725999956-0.184351205896-0.1365674879980.1810697433450.1533946606050.04233554857520.3393956355790.291666397003-0.1509336755730.0427660492137-0.3354328156860.434304213767-0.118767894592-0.0677966251207-0.0002564688677270.8961094297840.329823711757-0.01107226837260.870230984816-0.1107346324140.92031199147117.197261524448.131338321840.2565044895
30.02394361845150.0380349684203-0.03457388626720.01313364600550.03034280898430.00476121274775-0.265478887918-0.012674154236-0.2080488035920.434801227837-0.274045614171-0.0109630765722-0.2266722002830.2436140457836.70419171012E-61.047368213840.4080312165520.1329626124041.253551995-0.3129264187481.5205482178144.873647483227.962737158245.8454721098
40.4323467773210.0304314345810.1039545043660.2754935547080.2570463244270.388353787157-0.68441299013-0.6771111372880.1080950624280.480208386220.503044542993-0.08081983608520.1977553973670.428309145891-0.2400265186641.058952783780.4933018026720.1240431321891.225133461440.02657329112681.1857213436751.390361161322.489951936335.6930667621
50.02940182364510.1029661406480.0270776963380.1235578597330.1937051245830.26998783227-0.1880972348030.322283729270.128113908846-0.4633191488370.3699727638840.19883666219-0.5807683637770.5089378503790.04781917343680.6625479741060.03986086706310.05661739187120.7994388573240.02365058656460.71356336036564.94894917347.497302956438.53257854833
60.218714287415-0.0744689509442-0.05153712730350.0897952374535-0.2122615613693.77549527404-0.879997350796-0.699371964985-0.2446891420541.141852200270.0972408389921-0.1772779483150.1421553919271.76862597755-0.3232890049731.233983694150.7857409076040.411166031650.210363121326-0.06097936080491.2685873597423.354187712534.763765406548.5761356233
70.6122448476150.229809234547-0.1004028193090.229426891292-0.02097621227360.3831733474170.117453121950.102394317273-0.175216869297-0.331253002898-0.329024427837-0.08014974691030.0978625583450.324756956194-0.02746147476120.4356398640980.1860779737140.1065784553260.3240003264350.02308730497310.46119408010884.5839865324-14.0437105692-29.3292265007
80.6334263716010.107538253843-0.1765514964110.456000937091-0.03769104916490.0684432623321-0.261962840431-0.69837912905-0.4181450580790.738168538927-0.389530599407-0.2262588995010.5508454682580.921931872119-0.1242655041670.614204934974-0.07031124840180.08881829336410.4061893223790.1699327884540.59763886682786.5516510839-13.43519082-13.949422784
90.508937033324-0.0350988092356-0.2425067460260.06129648173110.0225037540780.383329947555-0.146165924905-0.7373108399970.5076338151380.103793256648-0.1645957363630.255881684983-0.03393317299680.3769617565850.1997070763280.580547360024-0.1362741607020.312533287941-0.008631673082490.324114943079-0.017095837356282.4803977747-8.59218575715-13.7232700749
100.142900676567-0.1239936394180.04801426011370.170270216234-0.04925520920320.08682174581080.0710950592778-0.3738785001150.08830333343690.66506674976-0.0664529111481-0.4459505006041.029012093120.09046865978250.0007873276015210.684847778816-0.01933198324810.06390670427730.6734509103510.1414678647750.58567596347874.6120642921-14.40568508920.972144292228
11-0.0158103502350.121256166677-0.06296711320580.133111218258-0.08291000578480.0774911637759-0.051434804492-0.206335915451-0.04638741664260.34598469501-0.3069703183740.3104245656370.2878939824860.225830466496-0.00548105177660.3763935435940.0003459161026580.04465384247240.407029337462-0.04902833307290.58162323018985.4357053988-4.23333067077-16.8298910005
120.0465599712745-0.006512380352060.05374859336280.0381244834537-0.03436877810260.05388322358410.384176237930.6143271372730.317239832432-0.2719077019980.0766002240832-1.19573082783-0.08670188534560.580300677455-0.0006341329119071.359098543990.1126714474020.1562176737290.815488816881-0.1041960475820.82271057697685.2736127542-27.4681433023-36.1940940852
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 3 through 113 )LA3 - 1131 - 115
22chain 'L' and (resid 114 through 210 )LA114 - 210116 - 212
33chain 'H' and (resid 2 through 17 )HB2 - 171 - 16
44chain 'H' and (resid 18 through 104 )HB18 - 10417 - 106
55chain 'H' and (resid 105 through 156 )HB105 - 156107 - 158
66chain 'H' and (resid 157 through 267 )HB157 - 267159 - 263
77chain 'A' and (resid 334 through 393 )AC334 - 3931 - 60
88chain 'A' and (resid 394 through 421 )AC394 - 42161 - 88
99chain 'A' and (resid 422 through 459 )AC422 - 45989 - 126
1010chain 'A' and (resid 460 through 494 )AC460 - 494127 - 161
1111chain 'A' and (resid 495 through 516 )AC495 - 516162 - 183
1212chain 'A' and (resid 517 through 529 )AC517 - 529184 - 196

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