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- PDB-8vu4: Structure of FabS1CE4-EPR-1, an elbow-locked high affinity antibo... -

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Basic information

Entry
Database: PDB / ID: 8vu4
TitleStructure of FabS1CE4-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor
Components(S1CE4 VARIANT OF FAB-EPR-1 ...) x 2
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 28, 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
B: S1CE4 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE4 VARIANT OF FAB-EPR-1 light chain
A: S1CE4 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE4 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,32731
Polymers94,3674
Non-polymers96027
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-254 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.863, 55.893, 87.016
Angle α, β, γ (deg.)80.050, 89.910, 82.700
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Antibody , 2 types, 4 molecules BACG

#1: Antibody S1CE4 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24134.004 Da / Num. of mol.: 2 / Mutation: K131Q and 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 S1CE4 VARIANT OF FAB-EPR-1 light chain


Mass: 23049.488 Da / Num. of mol.: 2
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, 228 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE 9.0, 10% PEG6000

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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: 2.27→85.69 Å / Num. obs: 43559 / % possible obs: 91.5 % / Redundancy: 2 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.115 / Rrim(I) all: 0.162 / Net I/σ(I): 8.3
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4024 / CC1/2: 0.508 / Rpim(I) all: 0.479 / Rrim(I) all: 0.677 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→55.4 Å / SU ML: 0.3678 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.9726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1899 4.85 %
Rwork0.2084 37275 -
obs0.2105 39174 91.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.27 Å2
Refinement stepCycle: LAST / Resolution: 2.35→55.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6385 0 45 201 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816608
X-RAY DIFFRACTIONf_angle_d1.06349002
X-RAY DIFFRACTIONf_chiral_restr0.05921023
X-RAY DIFFRACTIONf_plane_restr0.00951153
X-RAY DIFFRACTIONf_dihedral_angle_d16.94672319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.34761370.29092705X-RAY DIFFRACTION92.97
2.41-2.470.29631500.26842712X-RAY DIFFRACTION93.16
2.47-2.550.31781130.26142743X-RAY DIFFRACTION92.76
2.55-2.630.33021150.25362682X-RAY DIFFRACTION92.13
2.63-2.720.31051570.25272632X-RAY DIFFRACTION91.2
2.72-2.830.31971460.24142552X-RAY DIFFRACTION89.01
2.83-2.960.30141260.23372547X-RAY DIFFRACTION86
2.96-3.120.29791390.23362731X-RAY DIFFRACTION94.13
3.12-3.310.32471240.24252713X-RAY DIFFRACTION93.48
3.31-3.570.24471260.20612700X-RAY DIFFRACTION92.69
3.57-3.930.23971270.20132647X-RAY DIFFRACTION90.51
3.93-4.490.20731330.16242502X-RAY DIFFRACTION86.31
4.5-5.660.18331680.16942781X-RAY DIFFRACTION95.5
5.66-55.40.24161380.1972628X-RAY DIFFRACTION90.84
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)
13.05916500516-0.635908031347-0.6418533915045.06287802665-1.295625099496.067552747470.00608044129967-0.5113998815240.1543186229270.9081856363270.4192915206150.607011773963-0.667981015062-0.845715389348-0.1819812822630.5448002727230.1003663378280.03535244487340.580764787679-0.04565567984980.463826631541-32.33519.5825.714
22.73228144125-0.814520145278-0.1546071660274.54301260443-0.3746641382424.879292246680.0279663271277-0.4186711078040.2375752390160.6299691895040.0788644111034-0.0136624748576-0.614240845711-0.185945743761-0.1149440296710.5129387437130.0584806063163-0.0640373467260.43103818195-0.05539821268910.372009483932-24.92421.2685.837
33.575910845660.0456144362246-1.467056293612.37944582389-0.09784034338922.09781632098-0.03011406184890.0002907140137520.025414201095-0.0987252291678-0.0987794907891-0.1556455291760.08562458613880.1196767289350.1177035851350.2638551876110.0494843989138-0.04064983783660.252449398538-0.006391544142480.349922752974-3.80925.674-24.441
43.05609450001-1.81313830212-2.058866477845.91612738939-0.01523111799872.328357780820.0280622660645-0.3144910470050.171143086670.455254088366-0.0314751277777-0.40391046899-0.007143789113990.3610392645760.002150266981140.4392061415320.0310505077353-0.1416494269050.579000439897-0.008712426700110.339621027843-12.0783.97910.69
52.477917701660.9932820655792.143414040654.999353329883.109728194175.21532914049-0.1534234812220.1100562984080.0846174510369-0.04397761146460.05507493399650.0590109858046-0.1997908584470.2014332244170.08744325491550.1684263668860.01119321193530.07762316375250.3455938051960.042447772180.251507642309-21.258-1.563-10.5
63.41615009141-1.841652586310.642592883594.839202304020.2769539239316.95070132699-0.009660954273860.06667257542050.0821321879344-0.2134909939840.0118837401819-0.26266585601-0.150304158305-0.159508737596-0.01397408552010.268012498423-0.004376106213710.02032975774140.2130799529770.01945018435260.326461149656-20.808-8.282-23.57
74.52193271173-1.56169950538-0.07889963138472.955864152050.4024153120574.422167052330.2881681371050.7692797467990.201414540282-1.01016063341-0.2721761220420.412023226333-0.497137472486-0.575463081502-0.06740158607010.6527979503440.131327703637-0.1465507277680.6001049171440.005958298431840.4387968732-28.11321.097-47
86.166961189-1.58084020573-0.6259437582394.047796802640.2171825812715.778713213560.1976886386020.4716525865270.266952098401-0.83589758776-0.09131361117630.0441444412713-0.310873856934-0.318672562781-0.03575228281180.550493247330.00843568774971-0.0922380072930.389215729153-0.01330544842370.38955027224-24.68720.055-44.769
93.01120968763-0.2577273110330.02297590443193.72259419243-1.027910748032.23322915695-0.128581151846-0.106745705778-0.01304130654160.07688388309720.03880773225890.108917224680.0232329254258-0.07896392360410.08663991239210.2837081987750.049535573449-0.03076292706490.26677397259-0.01346620791470.279316312001-34.623-1.536-16.482
103.00980725656-0.471945374041.449791523643.128943649061.075592074494.763579288630.08789033365310.729046653068-0.332915569594-0.542282242495-0.06780161824960.05170610290650.3126417393450.0582718738933-0.02983409812440.592121389020.0262337750984-0.009479423593990.550756359762-0.09096355235360.328703583696-11.3164.002-50.022
114.93167596794-2.16127259134-0.3464404095125.031991930571.096134435874.20793382311-0.0860845259558-0.486842644423-0.1331150124620.1928931358110.03155566070030.079400062836-0.104045957054-0.2553151944230.04563283997160.228635001210.0105558167857-0.0232010702850.3100730005450.01645126412530.2877824630621.1812.82-16.628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:38 )B1 - 38
2X-RAY DIFFRACTION2( CHAIN B AND RESID 39:124 )B39 - 124
3X-RAY DIFFRACTION3( CHAIN B AND RESID 125:228 )B125 - 228
4X-RAY DIFFRACTION4( CHAIN C AND RESID 1:107 )C1 - 107
5X-RAY DIFFRACTION5( CHAIN C AND RESID 108:148 )C108 - 148
6X-RAY DIFFRACTION6( CHAIN C AND RESID 149:232 )C149 - 232
7X-RAY DIFFRACTION7( CHAIN A AND RESID 2:84 )A2 - 84
8X-RAY DIFFRACTION8( CHAIN A AND RESID 85:124 )A85 - 124
9X-RAY DIFFRACTION9( CHAIN A AND RESID 125:229 )A125 - 229
10X-RAY DIFFRACTION10( CHAIN G AND RESID 2:133 )G2 - 133
11X-RAY DIFFRACTION11( CHAIN G AND RESID 134:231 )G134 - 231

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