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- PDB-2jix: Crystal structure of ABT-007 FAB fragment with the soluble domain... -

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Basic information

Entry
Database: PDB / ID: 2jix
TitleCrystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor
Components
  • (ABT-007 FAB FRAGMENT) x 2
  • ERYTHROPOIETIN RECEPTOR
KeywordsRECEPTOR/IMMUNE SYSTEM / IMMUNE SYSTEM / RECEPTOR / TRANSMEMBRANE / RECEPTOR SOLUBLE DOMAIN / ANTIBODY / RECEPTOR-IMMUNE SYSTEM COMPLEX
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) / immunoglobulin complex / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / immunoglobulin complex / 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 / 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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Erythropoietin receptor / IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, Z. / Stoll, V.S. / DeVries, P. / Jakob, C.G. / Xie, N. / Simmer, R.L. / Lacy, S.E. / Egan, D.A. / Harlan, J.E. / Lesniewski, R.R. / Reilly, E.B.
CitationJournal: Blood / Year: 2007
Title: A Potent Erythropoietin-Mimicking Human Antibody Interacts Through a Novel Binding Site.
Authors: Liu, Z. / Stoll, V.S. / Devries, P. / Jakob, C.G. / Xie, N. / Simmer, R.L. / Lacy, S.E. / Egan, D.A. / Harlan, J.E. / Lesniewski, R.R. / Reilly, E.B.
History
DepositionJul 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABT-007 FAB FRAGMENT
B: ERYTHROPOIETIN RECEPTOR
C: ERYTHROPOIETIN RECEPTOR
D: ABT-007 FAB FRAGMENT
E: ERYTHROPOIETIN RECEPTOR
F: ABT-007 FAB FRAGMENT
G: ABT-007 FAB FRAGMENT
H: ABT-007 FAB FRAGMENT
L: ABT-007 FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)213,1499
Polymers213,1499
Non-polymers00
Water0
1
A: ABT-007 FAB FRAGMENT
C: ERYTHROPOIETIN RECEPTOR
F: ABT-007 FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)71,0503
Polymers71,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: ABT-007 FAB FRAGMENT
L: ABT-007 FAB FRAGMENT

B: ERYTHROPOIETIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)71,0503
Polymers71,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
3
D: ABT-007 FAB FRAGMENT
E: ERYTHROPOIETIN RECEPTOR
G: ABT-007 FAB FRAGMENT


Theoretical massNumber of molelcules
Total (without water)71,0503
Polymers71,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.954, 156.171, 164.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ABT-007 FAB FRAGMENT


Mass: 23348.893 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7Z3Y4*PLUS
#2: Protein ERYTHROPOIETIN RECEPTOR / / EPO-R


Mass: 24754.000 Da / Num. of mol.: 3 / Fragment: EPO RECEPTOR SOLUBLE DOMAIN, RESIDUES 25-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19235
#3: Antibody ABT-007 FAB FRAGMENT


Mass: 22946.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6GMX6*PLUS

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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: 3.55 Å3/Da / Density % sol: 65.33 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 50772 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 81.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→113.23 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.822 / SU B: 27.517 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.323 2506 5.1 %RANDOM
Rwork0.257 ---
obs0.26 46835 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.55 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å20 Å2
2--0.7 Å20 Å2
3---4.71 Å2
Refinement stepCycle: LAST / Resolution: 3.2→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14781 0 0 0 14781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02215158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6081.9620670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8551928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3823.522602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.071152385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4531593
X-RAY DIFFRACTIONr_chiral_restr0.0980.22321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211520
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.27264
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.210057
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2474
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.59833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.263215634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14636062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0254.55036
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.391 156
Rwork0.345 2773

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