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- PDB-4y5x: Diabody 305 complex with EpoR -

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Basic information

Entry
Database: PDB / ID: 4y5x
TitleDiabody 305 complex with EpoR
Components
  • Erythropoietin receptor
  • diabody 310 VH domain
  • diabody 310 VL domain
Keywordsprotein binding/immune system / diabody complex / receptor / protein binding-immune system complex
Function / homology
Function and homology information


erythropoietin receptor activity / regulation of complement activation / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration ...erythropoietin receptor activity / regulation of complement activation / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / hemopoiesis / decidualization / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / Erythropoietin activates RAS / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / receptor-mediated endocytosis / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / brain development / Regulation of actin dynamics for phagocytic cup formation / cytokine-mediated signaling pathway / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III ...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 / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Erythropoietin receptor / V1-11 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsMoraga, I. / Guo, F. / Ozkan, E. / Jude, K.M. / Garcia, K.C.
CitationJournal: Cell / Year: 2015
Title: Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands.
Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. ...Authors: Moraga, I. / Wernig, G. / Wilmes, S. / Gryshkova, V. / Richter, C.P. / Hong, W.J. / Sinha, R. / Guo, F. / Fabionar, H. / Wehrman, T.S. / Krutzik, P. / Demharter, S. / Plo, I. / Weissman, I.L. / Minary, P. / Majeti, R. / Constantinescu, S.N. / Piehler, J. / Garcia, K.C.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: diabody 310 VL domain
B: diabody 310 VH domain
C: Erythropoietin receptor
D: diabody 310 VL domain
E: diabody 310 VH domain
F: Erythropoietin receptor
G: diabody 310 VL domain
H: diabody 310 VH domain
I: Erythropoietin receptor
J: diabody 310 VL domain
K: diabody 310 VH domain
L: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,05330
Polymers205,06012
Non-polymers1,99318
Water50428
1
A: diabody 310 VL domain
B: diabody 310 VH domain
C: Erythropoietin receptor
J: diabody 310 VL domain
K: diabody 310 VH domain
L: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,99319
Polymers102,5306
Non-polymers1,46313
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: diabody 310 VL domain
E: diabody 310 VH domain
F: Erythropoietin receptor
G: diabody 310 VL domain
H: diabody 310 VH domain
I: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,06111
Polymers102,5306
Non-polymers5315
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)239.540, 239.540, 132.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 4 molecules CFIL

#3: Protein
Erythropoietin receptor / EPO-R


Mass: 25129.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19235

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Antibody , 2 types, 8 molecules ADGJBEHK

#1: Antibody
diabody 310 VL domain


Mass: 14222.671 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody
diabody 310 VH domain


Mass: 11912.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5NV67

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Non-polymers , 3 types, 46 molecules

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


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 4.64 Å3/Da / Density % sol: 73.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: sodium citrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→24.94 Å / Num. obs: 63411 / % possible obs: 95.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 73.51 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.061 / Net I/σ(I): 10.1 / Num. measured all: 219210
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.15-3.233.40.6271.61548745230.7050.3697.1
14.44-24.943.30.02430.4178153710.01570.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
Aimless0.2.17data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 3.15→24.94 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 3997 6.32 %
Rwork0.201 --
obs0.2035 63288 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13174 0 132 28 13334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313631
X-RAY DIFFRACTIONf_angle_d0.61418546
X-RAY DIFFRACTIONf_dihedral_angle_d9.9034751
X-RAY DIFFRACTIONf_chiral_restr0.0262053
X-RAY DIFFRACTIONf_plane_restr0.0032372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.1870.31511390.3172056X-RAY DIFFRACTION97
3.187-3.22580.35061390.3022055X-RAY DIFFRACTION96
3.2258-3.26660.35491370.29062042X-RAY DIFFRACTION97
3.2666-3.30940.34131400.28952065X-RAY DIFFRACTION96
3.3094-3.35470.29871340.27871999X-RAY DIFFRACTION95
3.3547-3.40250.28511400.27222093X-RAY DIFFRACTION97
3.4025-3.45310.36631380.26542020X-RAY DIFFRACTION96
3.4531-3.5070.33731390.26652066X-RAY DIFFRACTION96
3.507-3.56430.27941370.25712042X-RAY DIFFRACTION95
3.5643-3.62560.30781380.25652039X-RAY DIFFRACTION96
3.6256-3.69130.27141380.24752060X-RAY DIFFRACTION96
3.6913-3.76210.26771380.23932053X-RAY DIFFRACTION96
3.7621-3.83860.25071400.2252063X-RAY DIFFRACTION96
3.8386-3.92170.26681390.22442070X-RAY DIFFRACTION96
3.9217-4.01260.27741390.19792066X-RAY DIFFRACTION96
4.0126-4.11250.26091380.19892024X-RAY DIFFRACTION95
4.1125-4.22320.25871380.1912050X-RAY DIFFRACTION96
4.2232-4.34680.20351370.17482049X-RAY DIFFRACTION95
4.3468-4.48640.19531380.16712040X-RAY DIFFRACTION95
4.4864-4.64570.24041360.1592024X-RAY DIFFRACTION94
4.6457-4.83050.17891350.15522010X-RAY DIFFRACTION93
4.8305-5.04860.16871360.15552017X-RAY DIFFRACTION94
5.0486-5.31230.18831410.14822069X-RAY DIFFRACTION95
5.3123-5.64150.1961360.16082035X-RAY DIFFRACTION94
5.6415-6.07130.21961410.17542081X-RAY DIFFRACTION95
6.0713-6.67170.2371370.18622036X-RAY DIFFRACTION93
6.6717-7.6130.22391330.1821975X-RAY DIFFRACTION89
7.613-9.50250.17081380.16612053X-RAY DIFFRACTION91
9.5025-24.94220.23461380.19892039X-RAY DIFFRACTION87

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