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- PDB-8vu1: Structure of FabS1CE3-EPR-1, an elbow-locked high affinity antibo... -

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Basic information

Entry
Database: PDB / ID: 8vu1
TitleStructure of FabS1CE3-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor (trigonal form)
Components
  • S1CE3 VARIANT OF FAB-EPR-1 heavy chain
  • S1CE3 VARIANT OF FAB-EPR-1 light chain
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsSinger, A.U. / Bruce, H.A. / Pavlenco, A. / Ploder, L. / Luu, G. / Blazer, L. / Adams, J.J. / Sidhu, S.S.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159640 Canada
Other private United States
CitationJournal: Protein Sci. / Year: 2024
Title: Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones.
Authors: Bruce, H.A. / Singer, A.U. / Blazer, L.L. / Luu, K. / Ploder, L. / Pavlenco, A. / Kurinov, I. / Adams, J.J. / Sidhu, S.S.
History
DepositionJan 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S1CE3 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE3 VARIANT OF FAB-EPR-1 light chain


Theoretical massNumber of molelcules
Total (without water)47,1852
Polymers47,1852
Non-polymers00
Water00
1
A: S1CE3 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE3 VARIANT OF FAB-EPR-1 light chain

A: S1CE3 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE3 VARIANT OF FAB-EPR-1 light chain


Theoretical massNumber of molelcules
Total (without water)94,3694
Polymers94,3694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7380 Å2
ΔGint-54 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.608, 73.608, 153.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody S1CE3 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24135.057 Da / Num. of mol.: 1 / Mutation: F160W
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody S1CE3 VARIANT OF FAB-EPR-1 light chain


Mass: 23049.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 COMP IMMUNOL. 2003 JAN;27(1):55-77) NUMBERING
Source: (gene. exp.) Homo sapiens (human) / Plasmid: plasmid / Details (production host): PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M PCPT buffer pH 9.0, 25% PEG1500 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.93→153.89 Å / Num. obs: 10941 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 120.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.025 / Rrim(I) all: 0.079 / Net I/σ(I): 19.9
Reflection shellResolution: 2.93→3.11 Å / Redundancy: 10.6 % / Rmerge(I) obs: 2.384 / Mean I/σ(I) obs: 1 / Num. unique obs: 1727 / CC1/2: 0.496 / Rpim(I) all: 0.767 / Rrim(I) all: 2.507 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→63.75 Å / SU ML: 0.4206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2767 468 4.97 %
Rwork0.2355 8956 -
obs0.2375 9424 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.37 Å2
Refinement stepCycle: LAST / Resolution: 3.08→63.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 0 0 3149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383223
X-RAY DIFFRACTIONf_angle_d0.63344409
X-RAY DIFFRACTIONf_chiral_restr0.046509
X-RAY DIFFRACTIONf_plane_restr0.0204565
X-RAY DIFFRACTIONf_dihedral_angle_d16.34951095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.530.37531570.37222911X-RAY DIFFRACTION99.93
3.53-4.440.31681620.28132937X-RAY DIFFRACTION99.94
4.44-63.750.23911490.19653108X-RAY DIFFRACTION99.97
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)
18.50054609294-2.408601940230.2160671353047.656780512493.930746962959.11656092927-0.1140506177720.226376964547-0.687315187862-0.387574828679-0.107226665087-0.1566654242990.8612910952710.05178174786860.3051219587410.965018136131-0.02388383560120.1645913979270.7905142970080.006266026595860.757075898074-6.559126062214.2794588313.10827880556
20.07198447091590.121910764191-0.0538159420110.0994404007793-0.05701030023080.02500194169-0.0066674656254-0.999987226576-0.343371598570.419039505113-1.331181922970.10290120056-0.8148081571361.672910602220.8146746840531.089607560660.08047835108740.2916481694121.892730238430.01224233697541.421968654788.4154644361626.0777897736-7.079149139
32.214896815881.318077512143.880848403386.976434735421.700574598668.728190299650.01096778730050.231323029449-0.219357490857-0.3177449091790.3834298339070.220232871816-0.261991563917-0.0757617317031-0.4113945454420.5261060363120.04752326345610.03110972569081.00693946122-0.00772324367030.86315426375526.323128349327.7752878087-27.1568120951
43.960681670351.076563339570.3120791872486.483218834220.3756667382092.91792760202-0.150016516744-0.531653092353-0.2446803873920.688662212049-0.134647957313-0.5531978380440.3517251011170.202583393185-0.003621638245691.052837360980.0722060405736-0.1014611537961.251050483960.01755466876031.0563038158537.2923316533-4.10165797934-9.68389844667
51.701822071420.0548911631859-0.09969376967976.64659577624-0.5096553516781.809666486930.166572465698-0.8531961635980.09830545156830.431012767491-0.37157041842-0.502381131836-0.05509624719820.683255143583-0.00671949577460.768660732946-0.0337293990795-0.1706657468871.20086544303-0.06209493752170.934569892238.0370945734.16560752374-11.5796620088
64.027736116111.095704253720.04331421990918.34472237411-0.8345296989593.61016961129-0.1152371259580.359946956598-0.3487178467890.170247860105-0.1886994722320.415711894157-0.320102812514-0.15053722487-0.07025052093630.698279798222-0.0002074475840920.0284216194821.24842511203-0.1736475263930.91841533569436.148890553433.9716878314-20.6331725243
75.484100264550.7899191359090.6242958457412.48487403223-1.102464850982.98685162218-0.103590206643-0.5717199132240.4522619946520.6321583652540.1818477061940.0361822410926-0.507979546664-0.0400795498492-0.09242640159270.883782805083-0.02368821245580.04914392218091.17054306836-0.04466882520060.92645017521138.506816491835.8257817994-18.4476433603
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 121 )AA1 - 1211 - 110
22chain 'A' and (resid 122 through 133 )AA122 - 133111 - 122
33chain 'A' and (resid 134 through 230 )AA134 - 230123 - 219
44chain 'G' and (resid 2 through 91 )GB2 - 911 - 74
55chain 'G' and (resid 92 through 133 )GB92 - 13375 - 112
66chain 'G' and (resid 134 through 170 )GB134 - 170113 - 149
77chain 'G' and (resid 171 through 231 )GB171 - 231150 - 210

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