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- PDB-8vvo: Structure of FabS1CE2-EPR1-1 in complex with the erythropoietin r... -

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Basic information

Entry
Database: PDB / ID: 8vvo
TitleStructure of FabS1CE2-EPR1-1 in complex with the erythropoietin receptor
Components
  • Erythropoietin receptor
  • S1CE2 VARIANT OF FAB-EPR-1 heavy chain
  • S1CE2 VARIANT OF FAB-EPR-1 light chain
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Function / homology
Function and homology information


erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 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 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: S1CE2 VARIANT OF FAB-EPR-1 light chain
B: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE2 VARIANT OF FAB-EPR-1 light chain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8837
Polymers119,8255
Non-polymers582
Water00
1
A: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE2 VARIANT OF FAB-EPR-1 light chain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7754
Polymers72,7523
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1CE2 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE2 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1083
Polymers47,0722
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.246, 90.576, 214.850
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 19 or (resid 20...
d_2ens_1(chain "B" and (resid 8 through 127 or resid 129 through 229))
d_1ens_2(chain "C" and ((resid 2 through 3 and (name N...
d_2ens_2(chain "G" and (resid 2 through 50 or (resid 51...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYPHEPHEAA8 - 1278 - 116
d_12ens_1GLNGLNSERSERAA129 - 229118 - 218
d_21ens_1GLYGLYPHEPHEBC8 - 1278 - 116
d_22ens_1GLNGLNSERSERBC129 - 229118 - 218
d_11ens_2ILEILECYSCYSCD2 - 2322 - 212
d_21ens_2ILEILECYSCYSGB2 - 2322 - 212

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999433236976, 0.0110062067931, -0.0318130199774), (0.0235849608716, -0.445383703494, -0.895029109182), (-0.0240198761183, -0.895272148608, 0.444871695523)62.6874291067, -12.8540895945, 20.9424966389
2given(-0.997981249754, 0.0634234632322, 0.00329991680241), (-0.034372951222, -0.495713621383, -0.867805569122), (-0.0534034208975, -0.866167114295, 0.496892950996)64.4590537449, 12.256553203, -18.2265906494

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Components

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


Mass: 24022.906 Da / Num. of mol.: 2 / Mutation: K131Q, 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 S1CE2 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)
#3: Protein Erythropoietin receptor / EPO-R


Mass: 25679.996 Da / Num. of mol.: 1 / Mutation: residues 22-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Plasmid: pSCSTa / Details (production host): Hexa-histidine tag / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P19235
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MMT buffer pH 6.0, 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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2023 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.09→107.43 Å / Num. obs: 25960 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 75.6 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.152 / Rrim(I) all: 0.39 / Net I/σ(I): 5.3
Reflection shellResolution: 3.09→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.807 / Mean I/σ(I) obs: 1 / Num. unique obs: 4627 / CC1/2: 0.487 / Rpim(I) all: 0.734 / Rrim(I) all: 1.953 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→83.46 Å / SU ML: 0.4894 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.289 1299 5.03 %
Rwork0.2529 24545 -
obs0.2547 25844 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.96 Å2
Refinement stepCycle: LAST / Resolution: 3.09→83.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7879 0 2 0 7881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00438079
X-RAY DIFFRACTIONf_angle_d0.857111031
X-RAY DIFFRACTIONf_chiral_restr0.05021256
X-RAY DIFFRACTIONf_plane_restr0.00731411
X-RAY DIFFRACTIONf_dihedral_angle_d16.62782792
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.44533176658
ens_2d_2DCX-RAY DIFFRACTIONTorsion NCS1.37442265442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.220.40761390.40352688X-RAY DIFFRACTION99.4
3.22-3.360.3381570.36672695X-RAY DIFFRACTION99.41
3.36-3.540.37641390.34152695X-RAY DIFFRACTION99.37
3.54-3.760.36031490.32782710X-RAY DIFFRACTION99.1
3.76-4.050.3771320.30022670X-RAY DIFFRACTION98.21
4.05-4.460.25321350.21442674X-RAY DIFFRACTION96.13
4.46-5.110.24391750.19752726X-RAY DIFFRACTION99.62
5.11-6.430.26751250.22492820X-RAY DIFFRACTION99.73
6.43-83.460.2281480.19142867X-RAY DIFFRACTION97.45
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)
14.54886452624-0.0432942551159-0.6717612397522.38638654071-0.2265575172985.53117890882-0.01910885036230.23035683845-0.01301014406710.3810992208340.1536951099130.2923105331670.25249809674-0.376762182503-0.1040008290850.450439544285-0.02893894048010.0145680075710.409314820690.005913062494460.41971943807520.19080648930.39933669554929.5250754242
22.6765863286-0.164702624449-1.348830030613.493887127030.1943151011695.726075300710.1091074726240.571762965083-0.227934993773-0.0847975572157-0.3001098359870.123101422974-0.710047855219-0.09407472051690.1422065658550.439905573024-0.0354624595274-0.1497077783150.5579389752060.1415641346140.85392174559230.658701130119.47673611071.46100507325
35.18956653142-0.0927730262026-0.7687455268782.87932777522.859046477357.06137594012-0.109353463320.170502991362-0.420005797402-0.1558498883960.2947666246130.138852821182-0.198763648124-0.0683467270797-0.1466643155170.451390728009-0.00994092898521-0.009267526101340.30757055450.1451882803010.57445588658431.578151337616.6028037703-0.849525274195
47.09588615380.637315487096-2.553342272746.6865426387-2.268996788125.832124265890.0702979147531-0.527234301158-0.3747882369610.708639465255-0.0489265613774-0.4384053600230.06652618599050.800986950847-0.002416473594710.4612953938390.0432504871966-0.0859844210780.5024851567120.013668956510.47950179570343.7392272053-1.4003040966330.0323465818
55.720219498562.00981025802-3.941774207181.95187186226-2.303738237567.070054296290.218891572462-0.128351274673-1.320692515540.537870793344-1.19766244262-0.88746172004-1.095625343620.2599097683920.9555535910710.6490864273610.0730761406002-0.02869141851930.5112082506660.07294867400090.55920263386442.88358451466.609980900225.2463450501
65.614508318761.96089954745-0.4262516288596.336585804230.8712707297663.60056667174-0.223118791567-0.2665771900720.1440804620250.1559084916350.02766140470080.3673076454660.2510381677750.07239001939870.2036599692240.351683768488-0.00213114276990.1137029071640.4991874049770.02034016811720.48871399824142.228504077124.13915273346.67165113612
710.0492286319-3.567205266551.042276643687.86135929098-1.858485326284.05866004923-0.2675177327820.05753220042981.14682911454-0.3666743072780.0580990897274-0.160941108372-0.3391116487770.4335038617990.2513647937890.52413289653-0.08544720816230.01664640922230.5639037115960.02257783753880.52619344193443.27995705232.97185873622.80870793074
80.7591380189420.00481602763736-2.918040017832.89707344409-3.348921090727.896103374220.0317769491012-0.3917845290530.1041620598140.3533400260550.0018326514745-0.2574860291480.2141055284420.862864871237-0.1225486185860.606536778192-0.058475753901-0.04309024546480.8788073063830.0618079678620.58480762827541.8381939902-39.322349313431.7008035833
95.01493377732-0.4068345841050.5145986909684.86524214733-0.02133793380144.29545575317-0.0613884766137-0.05873393318040.39224278945-0.07828993739260.03082681522930.0647138487255-0.357833140104-0.04872715728980.1325273806810.40235967267-0.03355661527980.05844069299860.435202903468-0.004276450972940.40563276923130.5822157003-19.21507122544.133247833
104.39451023725-3.182167145561.434635124959.19160949632-0.2765491793642.741199122830.0987121608797-0.781441360326-0.764896942773-0.1706217193840.219626570920.8679233997070.7765179414760.0511583814358-0.2671404450810.677430574862-0.1016196578440.1554921416090.817330293969-0.05433435890930.83322152585816.1233117408-41.843114178631.9630908924
114.8874920966-2.005897919013.494376836453.254767844851.952941814077.358602458890.221282054163-0.560391407422-0.1988040296480.811287884347-0.2654739280370.5403086771990.591437409912-0.2636610725130.05933773563220.605226859371-0.110759562430.06413915571840.7967830085680.147937692970.71159300517319.7433704595-34.183712718937.1027082478
121.65438704101-1.300032885722.19128973111.41304038184-1.652657937986.69420918108-0.12172905104-0.797018659885-0.0611126603283-0.1045045805530.2610935723750.3525131878120.277800405416-0.936060605376-0.1319433996750.518590448493-0.0833089110886-0.06095227305740.692608827719-0.04733302689050.45933010205119.3111997198-35.705176538825.934138267
132.508857047251.231706579751.343073500372.816282712682.051479162585.835256174520.07047195635880.0462482907858-0.1985908750240.160608763076-0.0733213082253-0.3433923532130.1439489281760.0126825226256-0.1063638679720.4336890087260.0121639047482-0.05736409746170.4052983866890.05488660159730.59607755243820.5463360726-28.69793606032.45924481665
143.485336828381.181249703570.2763130032472.678024193511.84527969573.38179404054-0.2408160024520.3249987709240.166237803659-0.2114463374470.285591763695-0.2638000391960.3274192792810.18010805885-0.03864057916420.4220597946110.0563610800432-0.005865409665280.4802077750560.04632488675770.52868863230519.4673285904-30.4593380401-7.28831531629
153.27024591206-1.523325267062.845952406721.83235905684-2.849429160366.095482428250.348351486389-0.82055504166-0.6090233983840.346628836427-0.01670209821050.007861131693341.26376839611-0.252643882779-0.3083442576731.27608819025-0.228860373954-0.1454286362710.7772602216630.1145814492080.58614626317729.5665752915-14.596640115452.6010685266
162.8245362517-3.532461946941.430502572494.34700566323-1.365924538944.84699198166-0.6438842596770.6368677640941.26517229469-0.5900696003010.0838200661448-0.782197067845-1.156517816531.235843638560.4556136503061.04735200136-0.26951329947-0.02357821436720.7966300229860.195677372860.88115593010357.0601506553-21.627171579263.8886370316
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 127 )AA1 - 1271 - 116
22chain 'A' and (resid 128 through 171 )AA128 - 171117 - 160
33chain 'A' and (resid 172 through 230 )AA172 - 230161 - 219
44chain 'G' and (resid 2 through 107 )GB2 - 1071 - 90
55chain 'G' and (resid 108 through 133 )GB108 - 13391 - 112
66chain 'G' and (resid 134 through 194 )GB134 - 194113 - 173
77chain 'G' and (resid 195 through 232 )GB195 - 232174 - 211
88chain 'B' and (resid 8 through 133 )BC8 - 1331 - 115
99chain 'B' and (resid 134 through 229 )BC134 - 229116 - 211
1010chain 'C' and (resid 1 through 38 )CD1 - 381 - 32
1111chain 'C' and (resid 39 through 107 )CD39 - 10733 - 91
1212chain 'C' and (resid 108 through 133 )CD108 - 13392 - 113
1313chain 'C' and (resid 134 through 194 )CD134 - 194114 - 174
1414chain 'C' and (resid 195 through 232 )CD195 - 232175 - 212
1515chain 'I' and (resid 10 through 117 )IE10 - 1171 - 104
1616chain 'I' and (resid 118 through 223 )IE118 - 223105 - 202

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