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

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Basic information

Entry
Database: PDB / ID: 8vtr
TitleStructure of FabS1CE3-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor (orthorhombic form)
Components(S1CE3 VARIANT OF FAB-EPR-1 ...) x 2
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Function / homologyCITRIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,97012
Polymers47,1852
Non-polymers78610
Water4,558253
1
A: S1CE3 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE3 VARIANT OF FAB-EPR-1 light chain
hetero molecules

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

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

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

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

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


Theoretical massNumber of molelcules
Total (without water)287,82172
Polymers283,10712
Non-polymers4,71460
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation2_556-x+1/2,-y,z+3/21
crystal symmetry operation2_557-x+1/2,-y,z+5/21
Unit cell
Length a, b, c (Å)73.199, 74.275, 93.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 2 molecules AG

#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: PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 263 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThis is an open structure which forms a linear polymeric array
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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Citrate dibasic, 20% PEG3350. This was set up as a Fab/EPOR complex, however no EPOR was observed upon solving the structure.

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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: 1.96→74.28 Å / Num. obs: 37275 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Net I/σ(I): 18.5
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 6 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2602 / CC1/2: 0.855 / Rpim(I) all: 0.302 / Rsym value: 0.751 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→58.12 Å / SU ML: 0.2192 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 1749 4.7 %
Rwork0.1874 35461 -
obs0.1893 37210 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.12 Å2
Refinement stepCycle: LAST / Resolution: 1.96→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 49 253 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753303
X-RAY DIFFRACTIONf_angle_d0.97554493
X-RAY DIFFRACTIONf_chiral_restr0.062506
X-RAY DIFFRACTIONf_plane_restr0.0087572
X-RAY DIFFRACTIONf_dihedral_angle_d15.81741148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.020.29471560.24682903X-RAY DIFFRACTION99.71
2.02-2.080.26931520.24012912X-RAY DIFFRACTION99.97
2.08-2.160.27031220.21132942X-RAY DIFFRACTION100
2.16-2.240.27321480.20382891X-RAY DIFFRACTION99.93
2.24-2.340.25931280.20322959X-RAY DIFFRACTION99.97
2.34-2.470.24651200.20612951X-RAY DIFFRACTION99.9
2.47-2.620.25671320.21832941X-RAY DIFFRACTION99.87
2.62-2.830.28191550.2232953X-RAY DIFFRACTION99.97
2.83-3.110.23331550.20512932X-RAY DIFFRACTION99.9
3.11-3.560.2011450.18392978X-RAY DIFFRACTION99.68
3.56-4.480.18291550.15272980X-RAY DIFFRACTION99.46
4.49-58.120.22591810.16963119X-RAY DIFFRACTION99.55
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)
12.582787583850.188952147185-0.0213563872045.01376262137-0.6089202921061.712537013970.0610625961311-0.0156345023203-0.08709504383380.2232644038640.0193934355825-0.212627083884-0.08956847758350.12734153089-0.05843051295650.2598711053070.00542216508168-0.03715627550540.217523018535-0.0257726217870.28062553097913.0515661913-15.0945548627-9.28845294118
20.378928522088-0.9473279263130.4605730086485.56829648255-2.224110907371.730782777910.06221767350270.04485294412910.0912839462121-0.21330508001-0.0953226284809-0.106736896630.03093703145920.0399757848148-0.02306451957030.2216176638240.0145766927835-0.00378205351090.23797208017-0.04425939475070.31732591757416.5838945545-36.1673784481-7.93566533416
34.14663174723-1.741366202360.5270261233234.78765559795-1.263377843952.202949209070.00763480276148-0.180879940574-0.01468599089670.122423312055-0.05070075528590.006461249213580.01973093966630.08959182995570.03840583792250.211658492452-0.0178668303551-0.0007777588959040.252905840562-0.00850493826160.22762841616524.7927259386-54.01243715785.59174147338
45.102212637551.9842128779-2.360288177284.74913752261-0.2505018937484.02235747195-0.0383240677218-0.388176149787-0.3096456282250.327157672886-0.0822860576083-0.07618471195450.28472193290.4562806715510.1053170771610.2887648689690.07511293052650.01394864239950.3331303458610.01246987653830.28625860575345.4081251114-60.571572778229.8208085991
56.321402587571.63033001732.417397080492.262283237990.5110985316753.10637289027-0.0150166477062-0.02153013498120.00274019961532-0.0332019829284-0.0243520710306-0.0426689827328-0.0201382794233-0.08136386345890.05886593582930.1847167250070.01106518331230.02583066462160.1750560223970.01746582984120.22011647151838.287388772-50.9168531049-4.17602605286
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 107 )AA1 - 1071 - 99
22chain 'A' and (resid 108 through 148 )AA108 - 148100 - 135
33chain 'A' and (resid 149 through 228 )AA149 - 228136 - 215
44chain 'G' and (resid 4 through 126 )GE4 - 1261 - 103
55chain 'G' and (resid 127 through 232 )GE127 - 232104 - 209

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