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- PDB-8vuc: Structure of FabS1CE2-EPR-1, an elbow-locked high affinity antibo... -

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Basic information

Entry
Database: PDB / ID: 8vuc
TitleStructure of FabS1CE2-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor
Components
  • S1CE2 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: 2.5 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 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
A: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE3 VARIANT OF FAB-EPR-1 light chain
B: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE3 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,69913
Polymers94,1454
Non-polymers5549
Water84747
1
A: S1CE2 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)47,59110
Polymers47,0722
Non-polymers5198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE3 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1083
Polymers47,0722
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.389, 67.389, 168.232
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and (resid 1 through 11 or (resid 12...
d_1ens_2(chain "C" and (resid 2 through 47 or (resid 48...
d_2ens_2(chain "G" and (resid 2 or (resid 3 and (name...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLULYSLYSAA1 - 2321 - 221
d_2ens_1GLUGLULYSLYSBC1 - 2321 - 221
d_1ens_2ILEILECYSCYSCD2 - 2322 - 212
d_2ens_2ILEILECYSCYSGB2 - 2322 - 212

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.4981810474, -0.867066985683, 0.0032382633524), (-0.867071525248, 0.498169742894, -0.00372523417087), (0.00161682274181, -0.00466364700517, -0.999987818066)-33.6247831539, 19.4435270904, -35.6000103295
2given(-0.500384240545, -0.865803150752, 0.000718305582034), (-0.865802370479, 0.500384754518, 0.00116306421135), (-0.00136641382105, -3.99316735507E-5, -0.999999065659)0.0285679785401, -38.8985460001, -35.7329935619

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Components

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Antibody , 2 types, 4 molecules ABGC

#1: Antibody S1CE2 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24022.906 Da / Num. of mol.: 2 / Mutation: K131Q and E162G
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.: 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) / Details (production host): PSCSTA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 56 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MMT buffer pH 5.0, 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: 2.45→84.12 Å / Num. obs: 29855 / % possible obs: 94.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 56.95 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.057 / Rrim(I) all: 0.121 / Net I/σ(I): 7.5
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3577 / CC1/2: 0.417 / Rpim(I) all: 0.609 / Rrim(I) all: 1.291 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→55.14 Å / SU ML: 0.404 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.0312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 1950 6.98 %
Rwork0.2038 25998 -
obs0.2081 27948 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 27 47 6498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826588
X-RAY DIFFRACTIONf_angle_d1.05558980
X-RAY DIFFRACTIONf_chiral_restr0.05731026
X-RAY DIFFRACTIONf_plane_restr0.00971146
X-RAY DIFFRACTIONf_dihedral_angle_d18.00522287
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.645493548843
ens_2d_2DCX-RAY DIFFRACTIONTorsion NCS0.632035228082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35691460.33971950X-RAY DIFFRACTION100
2.56-2.630.37391460.3011956X-RAY DIFFRACTION99.95
2.63-2.710.34141060.27871452X-RAY DIFFRACTION72.6
2.71-2.80.35511480.26871937X-RAY DIFFRACTION98.49
2.8-2.90.41051350.27921901X-RAY DIFFRACTION97.6
2.9-3.010.29491380.27331950X-RAY DIFFRACTION99.81
3.01-3.150.33011430.23551989X-RAY DIFFRACTION99.95
3.15-3.320.30371460.25051974X-RAY DIFFRACTION100
3.32-3.520.29711260.23211641X-RAY DIFFRACTION84.02
3.52-3.80.25581340.21811703X-RAY DIFFRACTION86.94
3.8-4.180.23491330.1821711X-RAY DIFFRACTION87.19
4.18-4.780.2251450.15671936X-RAY DIFFRACTION99
4.78-6.020.23641430.16651968X-RAY DIFFRACTION100
6.03-55.140.22171610.16071930X-RAY DIFFRACTION99.15
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)
19.059524967826.28249693754-3.9318257378410.3191003354-0.8506051248069.56033977670.01428238543010.993408277010.2611327252470.2640412571220.438301558088-0.539059875079-0.1591481989530.883380239176-0.4230229867870.371468156509-0.009385434006220.04067225715040.71867974166-0.02480996494980.474488835951-15.59184012679.47321411461-12.5482288328
24.316868295911.01656898666-1.827877210266.49600682692-1.380769135246.32940878726-0.117763471561-0.04028518938090.188865035317-0.01314949803070.0847497694006-0.141399019050.0627941609529-0.0682635849669-0.01326555146510.241921524150.00456955937157-0.00129332158850.235778050215-0.05490606975640.304912528766-41.996711614514.21099825910.5904869688
36.508641111122.40007637742-0.7636430639548.21674564127-0.07162857562614.52343346547-0.381450925740.782361810148-1.05560254507-0.3493988109670.479674973848-1.125318362070.7958575378460.380989870285-0.1488037938060.6058317600560.04368287338710.1469560413020.495354681463-0.1580312847390.71113260954-26.7417931574-11.3209426182-11.7152425452
44.682513379190.5320281881341.33712583379.264459117140.4772067143052.70231800772-0.5758772188481.46149085076-0.802994238307-1.478351026910.270457595821-0.1093410427530.09300058481141.045873604430.3072660886540.562918890687-0.01874861487370.06927604163330.900606210226-0.05215022826250.447362231529-24.1083206852-1.26389057333-19.4058929526
55.08645223797-3.24916702147-1.410709184346.75377035488-1.004139249642.50300376835-0.2323903603340.440155642355-0.276237092282-0.02095472111310.1529610410830.6536672219150.314747059564-0.09625387286350.06707576013730.42226966859-0.1432183208910.009640480879150.358899942127-0.03092041990190.364813624348-52.00782612576.967479441971.99686552192
63.99452737301-0.8006117941810.01370318500937.316036500160.2040216203512.56537124764-0.34825173553-0.217458448706-0.198032680233-0.2577757461480.1805051789371.17320545920.120633242628-0.2450241760190.1665153418580.431815794496-0.09602149918840.06066883922890.3455816411350.007659554160420.496592925292-55.49145870068.773137961433.94740235584
73.874771466732.60298419052-1.117927104644.89085833466-3.628265597279.601981950160.3557135326770.447031054638-0.5109142499860.2426872367290.1462442280381.092634156330.99234776296-0.818761639089-0.5864785300210.577338377391-0.204703523733-0.04951810129250.735414742504-0.000258681173990.875671156497-37.008966714135.6602482278-27.5943722466
86.470420553050.921278227916-3.106189641789.25840444405-3.949258293949.343552188040.975910411662-0.8166380550390.3070547220461.15012903494-0.5465699561461.12093947490.281300745578-0.532314541419-0.4713506678640.671770337411-0.2172657619560.01364623097110.542423050623-0.008291884581970.585677304553-34.244892294539.6498859312-20.5074430611
93.56598643196-0.3609099992290.3510475984064.5100316836-1.257202657592.391160754730.106474351186-0.176496551485-0.2677069065880.146159756149-0.01591933115510.1666706121490.1253510862340.0731457469767-0.07226833549720.299249357196-0.0225108347527-0.02175642108410.354243134470.03124678013580.318043614175-24.745422367858.3734816172-42.9343620206
105.83413055423-3.753508856590.988489911233.624095879912.228123248246.88292049949-0.499539467818-0.09161227629950.885791093384-0.998362670274-0.08014789693540.39344505678-1.185578770620.5923414345530.3440968923960.505077362078-0.098689005701-0.1134100112240.5220658858770.1189549914810.46272519234-26.943040298169.3893670426-53.5363764629
119.321504286672.1176391382-1.697811365343.585189511090.6803250952495.219547273780.639203974538-0.876241398808-1.050977504970.297917649666-0.120015518844-0.07231944315610.788198478980.256608285258-0.4620710625080.6903467143250.12257604525-0.09299572842850.5193176260840.2125246487930.72770343654-10.710909416536.5703676696-22.7432336889
123.889825277441.005539510290.3391523653696.06798373689-1.578717085882.496308903590.0627911129292-0.33098429123-0.1080099834810.123309566105-0.202252701035-0.4343911568170.5316932970520.2941788695270.2723722148390.4233663580450.118072355086-0.04168348170030.5914810476250.06755658153210.415597919973-11.200497039843.028837209-27.8111746801
134.12959985421-0.370338478871-0.7511039890337.14236392741-0.6022377471974.444103113320.0474656816497-0.5473544725050.5404348795530.130443107107-0.0274199779401-0.146922798192-0.03389644547390.2081751030830.02382289839890.219342055354-0.04461334415090.03496406852980.452291188370.01047715835690.34971432861-15.983377253871.2682675084-37.9110523785
147.63291583383-5.85125837316-0.4320350214119.176223429980.976470326082.62820748173-0.0126654464982-0.005703045348450.682976380223-0.234424198665-0.351261108773-0.262212355244-0.1533826586120.2203524168350.3468892549420.2614526517-0.0277551234022-0.02695108118960.4673847986170.08271887039440.360210159489-13.592148028871.9732537665-39.574454875
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 232 )AA122 - 232111 - 221
33chain 'G' and (resid 2 through 106 )GD2 - 1061 - 89
44chain 'G' and (resid 107 through 122 )GD107 - 12290 - 101
55chain 'G' and (resid 123 through 183 )GD123 - 183102 - 162
66chain 'G' and (resid 184 through 232 )GD184 - 232163 - 211
77chain 'B' and (resid 1 through 38 )BE1 - 381 - 33
88chain 'B' and (resid 39 through 106 )BE39 - 10634 - 98
99chain 'B' and (resid 107 through 217 )BE107 - 21799 - 206
1010chain 'B' and (resid 218 through 232 )BE218 - 232207 - 221
1111chain 'C' and (resid 1 through 91 )CF1 - 911 - 75
1212chain 'C' and (resid 92 through 133 )CF92 - 13376 - 113
1313chain 'C' and (resid 134 through 183 )CF134 - 183114 - 163
1414chain 'C' and (resid 184 through 232 )CF184 - 232164 - 212

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