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- PDB-8vui: Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8vui
TitleStructure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor
Components
  • (S1CE 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-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
CITRIC ACID / AMMONIUM ION / Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSinger, A.U. / Bruce, H.A. / 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 1.1Oct 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: S1CE VARIANT OF FAB-EPR-1 heavy chain
G: S1CE VARIANT OF FAB-EPR-1 light chain
D: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71218
Polymers72,8263
Non-polymers88715
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-121 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 71.930, 197.020
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 S1CE VARIANT OF FAB-EPR-1 heavy chain


Mass: 24096.021 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)
#2: Antibody S1CE 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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Protein / Sugars , 2 types, 2 molecules D

#3: Protein Erythropoietin receptor / EPO-R


Mass: 25679.996 Da / Num. of mol.: 1
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 236 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.2 M Ammonium Citrate dibasic, 20% PEG2000 monomethyl ether, pH 5.2
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: Jun 21, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.06→98.51 Å / Num. obs: 46837 / % possible obs: 92.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.21 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 9.3
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2699 / CC1/2: 0.723 / Rpim(I) all: 0.506 / Rrim(I) all: 1.298 / % possible all: 69.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→98.51 Å / SU ML: 0.2383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 1927 4.29 %
Rwork0.1973 43041 -
obs0.1991 44968 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→98.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 49 222 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734891
X-RAY DIFFRACTIONf_angle_d0.94346674
X-RAY DIFFRACTIONf_chiral_restr0.0578756
X-RAY DIFFRACTIONf_plane_restr0.0084855
X-RAY DIFFRACTIONf_dihedral_angle_d17.09991702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31631430.27283207X-RAY DIFFRACTION99.61
2.15-2.210.30841430.25483189X-RAY DIFFRACTION99.61
2.21-2.280.432920.35152056X-RAY DIFFRACTION63.38
2.28-2.350.2731430.24023200X-RAY DIFFRACTION99.46
2.35-2.430.28091430.23083179X-RAY DIFFRACTION99.16
2.43-2.530.26891440.23393205X-RAY DIFFRACTION99.05
2.53-2.650.25181430.21893218X-RAY DIFFRACTION99.97
2.65-2.790.26421220.20742733X-RAY DIFFRACTION83.85
2.79-2.960.22781470.21043259X-RAY DIFFRACTION99.91
2.96-3.190.281440.21923230X-RAY DIFFRACTION99.76
3.19-3.510.21961330.19052974X-RAY DIFFRACTION90.42
3.51-4.020.2261270.1862814X-RAY DIFFRACTION85.1
4.02-5.060.19381490.14693319X-RAY DIFFRACTION99.71
5.06-98.510.23561540.18883458X-RAY DIFFRACTION98.8
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)
10.810505434873-0.559651687710.4849767777661.5677553835-0.9109950259096.02540743214-0.07136670059450.132297766851-0.223808140035-0.09169002832950.00248671299470.03774413699760.8245191032490.09815301899450.05025430475230.455294930998-0.05793493280140.01871833773480.29924519851-0.004206319241980.326174782391-3.71207221777-40.136832887313.7163411485
26.399364743850.1117931630731.384523336133.23487889769-2.695296010357.04934338992-0.183934391371-0.6443566683131.364225407591.71730372772-0.0264732981054-0.158239821798-0.599069684573-0.3893511486950.1236961563040.4718077846590.0228454355244-0.07287834817380.287971124685-0.09080447546370.476043316449-2.18931340041-23.790737484354.9986026879
34.51623993565-1.80506142506-2.588697835937.203845456171.547232435775.754087669830.180683730196-0.07424262098320.161396240333-0.0159087805104-0.09900088165930.3743585128090.159271556632-0.130335390385-0.0817703910960.1919923303480.00682710264268-0.06110483307620.2008565937770.02120381938270.272682882101-5.08852256643-29.873729650246.4903581248
46.28546157344-2.60874840498-1.872086615653.338778712681.766422349615.14245127257-0.3290606334010.1203667298720.3034353590650.5320845276440.143621380042-0.432795122234-0.2349866309760.3647611175130.14544401890.499210195044-0.146781888824-0.07464904256990.3842759122220.08453525281620.392019627639-0.576199670924-13.694555143616.0434596714
53.96117639844-2.24401076038-0.2565208180153.125495610371.316264184614.342232376450.05553316504470.4335680785660.334777861769-0.0463110162602-0.0762587527261-0.339468982886-0.1489945399770.1579184157150.008885000649140.313264950282-0.0796514282902-0.04197148939570.3493248502990.06602014590540.26266635329-5.94551061888-17.72085941128.44774302953
65.10142954573-4.11323126216-0.225257428876.061084435261.129056620062.361836852720.005441321492950.4189845027780.184556758732-0.0405102263858-0.0810630828207-0.340387661046-0.007966390298820.08797263447250.04748973349570.328939132858-0.103883562774-0.03206469114880.3713008617820.06029118736510.281709339118-4.52312425351-20.479503311612.822340733
70.5267529557511.257538306611.895415297572.846577821333.933065310896.53774550596-0.39261809790.05529044190030.386717103822-0.3743473811930.02855678263910.390880976843-1.21165910591-0.2463742835460.3493001488160.5770460818210.0606577535104-0.09355654220020.3187125566460.009892925158170.412666299428-5.60917158858-9.475398616530.6235795295
85.19578288031-0.7417669475411.641802643037.77467605257-2.023304928054.725512943910.234064629586-0.156398567352-0.2779530381550.00142994684782-0.133214867362-0.08415790621720.2159916567380.108030703202-0.07466610941340.2372058091480.038045685778-0.03300061397790.188818576304-0.03152626358530.2424476161374.92966110212-19.586350603246.7381014919
99.534473290222.039540208966.411385490515.769412791780.1490162746788.73050230691-0.119527584681-0.3898390178940.476233976577-0.400227822091-0.234490780789-0.946711020043-0.262930778230.5187638243420.3155913613350.221882443140.002773402675350.06100977853730.3406637724180.01345736727590.51883852327813.2443053571-18.998761176443.2709166669
105.20833599569-1.685196134123.462742044216.61714241541-2.058531713336.324150540880.168753809242-0.289067185874-0.1646266561380.30478880645-0.125130455982-0.376031108287-0.325015496013-0.0488726432142-0.03528343095040.226386598483-0.005600819320050.0339438203760.219808516760.01876739611970.2372657359826.2670835844-16.853920717847.1032366049
114.27785238322.32728848325-1.314006685852.78188814558-1.908701019634.10013369741-0.3240035079110.54491043581-0.112376647828-0.6203781724580.124140553114-0.04302528993770.789958702648-0.5716867476040.1904112606320.586369784967-0.0627365809369-0.059187232840.492679654082-0.06674163556970.30391069121-3.22035319488-30.337903915-17.3084238879
122.29411589552-0.7992482975411.169966889396.25790592722-4.378390509254.54190563882-0.4066065396970.1379304155670.659642154745-0.2096398262230.290792016613-0.198414429005-0.0159557766983-0.2040826486260.1427757308430.397847429752-0.0884223202714-0.1193702786930.523696216052-0.04751644512350.4938799472-4.5935882031-14.3430237387-24.024918437
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 133 )AA1 - 1331 - 122
22chain 'A' and (resid 134 through 148 )AA134 - 148123 - 135
33chain 'A' and (resid 149 through 230 )AA149 - 230136 - 217
44chain 'G' and (resid 1 through 18 )GH1 - 181 - 18
55chain 'G' and (resid 19 through 91 )GH19 - 9119 - 75
66chain 'G' and (resid 92 through 121 )GH92 - 12176 - 101
77chain 'G' and (resid 122 through 133 )GH122 - 133102 - 113
88chain 'G' and (resid 134 through 170 )GH134 - 170114 - 150
99chain 'G' and (resid 171 through 183 )GH171 - 183151 - 163
1010chain 'G' and (resid 184 through 231 )GH184 - 231164 - 211
1111chain 'D' and (resid 8 through 69 )DO8 - 691 - 62
1212chain 'D' and (resid 70 through 220 )DO70 - 22063 - 198

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