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- PDB-8vvm: Structure of FabS1CE1-EPR1-1 in complex with the erythropoietin r... -

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Basic information

Entry
Database: PDB / ID: 8vvm
TitleStructure of FabS1CE1-EPR1-1 in complex with the erythropoietin receptor
Components
  • (S1CE1 VARIANT OF FAB-EPR-1 ...) x 2
  • Erythropoietin receptor
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 activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / 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 activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / 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 / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / 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
DI(HYDROXYETHYL)ETHER / Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S1CE1 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE1 VARIANT OF FAB-EPR-1 light chain
B: S1CE1 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE1 VARIANT OF FAB-EPR-1 light chain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,65421
Polymers119,8275
Non-polymers82716
Water543
1
A: S1CE1 VARIANT OF FAB-EPR-1 heavy chain
G: S1CE1 VARIANT OF FAB-EPR-1 light chain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0839
Polymers72,7533
Non-polymers3296
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S1CE1 VARIANT OF FAB-EPR-1 heavy chain
C: S1CE1 VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,57112
Polymers47,0732
Non-polymers49810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.165, 91.612, 216.735
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 13 or (resid 14...
d_2ens_1(chain "B" and (resid 8 through 30 or (resid 35...
d_1ens_2(chain "C" and (resid 3 through 17 or resid 19...
d_2ens_2(chain "G" and (resid 3 through 17 or resid 19...

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_1GLYGLYTHRTHRAA8 - 1458 - 134
d_12ens_1GLYGLYSERSERAA148 - 229137 - 218
d_21ens_1GLYGLYSERSERBC8 - 2298 - 218
d_11ens_2GLNGLNASPASPCD3 - 173 - 17
d_12ens_2VALVALCYSCYSCD19 - 23219 - 212
d_21ens_2GLNGLNASPASPGB3 - 173 - 17
d_22ens_2VALVALCYSCYSGB19 - 23219 - 212

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999183740021, 0.00755370022711, -0.0396836904822), (0.0319107825945, -0.454770841833, -0.890036619119), (-0.0247700551396, -0.890576455466, 0.45415858611)64.4809127339, -12.9958389998, 21.0858307757
2given(-0.998516385634, 0.0541764100016, -0.00547213118361), (-0.0225268182044, -0.502486484601, -0.864291545287), (-0.0495738850801, -0.86288600023, 0.502961410572)65.9425123622, 11.9705861845, -18.3970063798

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Components

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Protein , 1 types, 1 molecules I

#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

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Antibody , 2 types, 4 molecules ABGC

#1: Antibody S1CE1 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24023.959 Da / Num. of mol.: 2 / Mutation: 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 S1CE1 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, 19 molecules

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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
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 EIGER2 X 16M / Detector: PIXEL / Date: Apr 6, 2023 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.85→108.37 Å / Num. obs: 34880 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 79.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Net I/σ(I): 10.8
Reflection shellResolution: 2.85→2.99 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4546 / CC1/2: 0.787 / Rpim(I) all: 0.423 / Rrim(I) all: 1.126 / % 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: 2.9→84.38 Å / SU ML: 0.4299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 1584 4.79 %
Rwork0.2191 31493 -
obs0.2216 33077 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.64 Å2
Refinement stepCycle: LAST / Resolution: 2.9→84.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 43 3 7940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00978121
X-RAY DIFFRACTIONf_angle_d1.217411055
X-RAY DIFFRACTIONf_chiral_restr0.06311253
X-RAY DIFFRACTIONf_plane_restr0.01631404
X-RAY DIFFRACTIONf_dihedral_angle_d18.60462831
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.26936621334
ens_2d_2DCX-RAY DIFFRACTIONTorsion NCS1.36265251559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.29511460.28682799X-RAY DIFFRACTION99.86
2.99-3.10.37321570.31182801X-RAY DIFFRACTION99.93
3.1-3.220.38511440.34012830X-RAY DIFFRACTION99.87
3.22-3.370.38391620.29832796X-RAY DIFFRACTION99.83
3.37-3.550.30311200.25672862X-RAY DIFFRACTION99.6
3.55-3.770.32251360.25432809X-RAY DIFFRACTION99.33
3.77-4.060.29851290.24822885X-RAY DIFFRACTION99.97
4.06-4.470.24171450.18612849X-RAY DIFFRACTION99.97
4.47-5.120.22731490.16792893X-RAY DIFFRACTION99.9
5.12-6.450.23481440.19752903X-RAY DIFFRACTION99.77
6.45-84.380.23821520.18383066X-RAY DIFFRACTION99.78
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)
13.738053464620.2719320522790.3378357115753.68583386946-1.416975830446.809147357240.2164866480630.0431771258548-0.1992108769660.303509775864-0.1893604817950.2922823759270.22232415641-0.53482160908-0.04858168013550.453926930879-0.04098609412090.005428404777080.439419229928-0.07189383176520.54051365037721.21900679490.62369150846529.8720692055
20.2679835082410.696004967413-0.4457530697552.27805319146-1.157661515571.450032407470.558966042741-0.302511100031-0.2283682175230.401936679578-0.3684186891450.420273856173-0.624363446660.184241740158-0.2911004102860.562201225283-0.0265596318795-0.01430324652340.74424514612-0.01436283563490.79782534842323.65895891923.00830952067.60892588835
32.59791231833-0.18988435162-0.02920721623453.717766039570.4340641228785.8503386688-0.04168823981950.4142394811290.189775937436-0.3725855470270.2961336370180.0430822625356-0.170742489926-0.048973973466-0.2683594612550.3549109208820.04014962169330.02622455121030.6222478054720.05791335470040.62166337478133.469090309817.6655400257-0.614106999309
47.658488257540.809102606139-2.643039657954.87317863101-3.013232020224.64418354509-0.0612955810215-0.844595930855-0.2030997679920.6962508425970.0536514945206-0.200015592634-0.04694545660180.5426277313040.01988302510520.6198275582810.114576609351-0.160895721730.461157667625-0.04179867771690.57492780997944.5510601048-1.2164854067930.3527287911
52.1889700040.377081280658-0.5572071532141.08902797654-2.121163237736.46626299882-0.1228088150880.280760817753-0.03596460127570.0491938401383-0.09553508813570.01631962126270.2941010523890.2799643250350.2185164353820.430706741313-0.01415719786320.01202255198510.262808508703-0.05555433271010.56348722563840.839992503716.094052863413.9715774447
64.26149217613-1.308899941490.6636921969787.83689910348-2.159853349642.785530176580.08791948663210.2484889278770.1888720553270.0863567248535-0.0852971059670.168096976811-0.2204341604080.11933714718-0.009312871452160.4167434092590.07181865059960.08128264389670.577441536988-0.02656720229460.52037257882145.581997297627.26197557166.29401841004
7-0.22274277976-0.516370436768-0.2602892320913.05693834322-4.258722230869.07226140921-0.127413692945-0.2831921463530.001215271897580.221955466201-0.106488220624-0.3871790668070.2470066276911.074292015430.2657360081890.651277930220.0611553081166-0.06763281319511.032510090840.01883571490610.70591470588642.4178416023-39.6281107731.9729440304
81.943893358740.610903735979-1.362888800735.40053878594-1.377032993453.70533137293-0.01248540424780.07775999157040.11434294842-0.165796225395-0.08346701856730.451873956097-0.129732857370.07238445393740.07643911073290.3144233083980.00715587160833-0.0346928178510.569846524345-0.07938982651020.58813181950531.5603537009-19.84132137124.00790117348
95.81595908414-1.729167374420.7325123617617.919705946172.052680586686.62634599825-0.155675343428-0.346094985631-1.12956756910.545497007929-0.2189340427210.9018025954681.09665131461-0.4773298531910.352536763770.730960025062-0.1419086134550.2072109941310.7512409946130.03191635051050.65830965018417.0555168814-39.542305463633.1235295776
108.3655530621.04408705167-0.7683187270153.45218192580.6772132819473.501653502720.421065693893-0.7855676592090.3226353334520.743027392316-0.3333996636270.306895039406-0.743118043789-0.363151437537-0.07340025921530.683987555740.06734693874930.05064834174590.7572518536530.05161978199010.71823266919423.4888401819-30.867868229940.0379717917
113.4953312882-0.6530494525210.3263249700783.57313728645-0.7522542174086.558578650530.151268055767-0.491958555619-0.1707788752890.696225720329-0.02789420577170.5634095218470.85919177203-0.373567484229-0.06267199323590.756900197662-0.1213380475190.1173286181620.901944795331-0.02087700358780.69458652685717.2652443815-35.651237027735.9646564284
121.30383180455-0.11574286049-0.6885355217430.505781225657-0.6892098594950.9182653084270.0602384564067-0.283881239954-0.108571881953-0.01346110129180.07080571459930.1704223428390.061011408093-0.282412223054-0.1564647290270.687842431074-0.04692705304270.0006747323476780.731247308995-0.1054185489010.71338172925319.7212263273-35.648657970226.2895053516
131.03459352921.03029516022-0.1336751735692.956305885021.504918448276.446422746510.0182004743077-0.2067039959740.0211174708013-0.2029929380770.1689984649550.149168301529-0.07118817668450.312921654641-0.03837969206350.3680186085060.0899717044555-0.03250184117140.566107158338-0.05603822807070.64680571681321.903998469-28.0118785756-0.657696283681
141.112710921830.2047867924540.2654382473721.509209246050.6375805106656.51538094124-0.1405422955340.0305856680829-0.05686604947040.0686064037858-0.0257978423612-0.1764454310730.3356986165590.427367207096-0.03663203038930.4940005815020.0250353807608-0.04073292782620.488370022004-0.0190004557110.67482816760322.2334004181-31.36965161571.5970480295
153.67930027854-2.99763415711-5.542777681173.368768386964.306728415869.370169201890.3027454869830.666917811787-0.131991705885-0.292417336697-0.156979111794-0.114061469951-0.823559022855-0.622996478257-0.01285473983460.532430785006-0.0363081601946-0.07017215374240.5937133431780.03195686588540.51359048577715.0088214814-28.7706929892-6.84544033798
164.27288744578-0.10067936840.6048184780952.26588994282-1.466978755212.803452060290.696702067139-0.788084030826-0.565012360170.405190379884-0.229223701777-0.2627207361241.35175690126-0.245442134932-0.4753093922041.38519633679-0.222309213749-0.2351279245190.7348922487460.05129976518050.63733536230230.3188527248-14.69582481153.0250001037
173.77248209524-1.7079179561.503576042214.9657573661-0.3603437787874.16640696126-0.308026912170.3321998726160.620082244377-0.7962323862330.272044828103-0.816691310989-0.9101402158980.7325267984990.08398203251651.10372316679-0.244070710593-0.001392679265460.6325488550960.01365763216960.84925316494657.4640654278-21.582206819663.816323353
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 126 )AA1 - 1261 - 115
22chain 'A' and (resid 127 through 138 )AA127 - 138116 - 127
33chain 'A' and (resid 139 through 230 )AA139 - 230128 - 219
44chain 'G' and (resid 1 through 107 )GC1 - 1071 - 91
55chain 'G' and (resid 108 through 148 )GC108 - 14892 - 128
66chain 'G' and (resid 149 through 232 )GC149 - 232129 - 212
77chain 'B' and (resid 8 through 133 )BE8 - 1331 - 115
88chain 'B' and (resid 134 through 229 )BE134 - 229116 - 209
99chain 'C' and (resid 3 through 44 )CF3 - 441 - 36
1010chain 'C' and (resid 45 through 75 )CF45 - 7537 - 59
1111chain 'C' and (resid 76 through 107 )CF76 - 10760 - 89
1212chain 'C' and (resid 108 through 133 )CF108 - 13390 - 111
1313chain 'C' and (resid 134 through 170 )CF134 - 170112 - 148
1414chain 'C' and (resid 171 through 208 )CF171 - 208149 - 186
1515chain 'C' and (resid 209 through 232 )CF209 - 232187 - 210
1616chain 'I' and (resid 10 through 113 )IJ10 - 1131 - 100
1717chain 'I' and (resid 114 through 222 )IJ114 - 222101 - 202

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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