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- PDB-5bo1: Crystal structure of a human Jag1 fragment in complex with an ant... -

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Basic information

Entry
Database: PDB / ID: 5bo1
TitleCrystal structure of a human Jag1 fragment in complex with an anti-Jag1 Fab
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Protein jagged-1
KeywordsSignaling protein/Immune system / Jag / Notch / antagonist / Signaling protein-Immune system complex
Function / homology
Function and homology information


endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / cardiac right ventricle morphogenesis / inhibition of neuroepithelial cell differentiation / distal tubule development / neuroendocrine cell differentiation / aorta morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / T cell mediated immunity / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / endothelial cell differentiation / neuronal stem cell population maintenance / pulmonary valve morphogenesis / cell fate determination / negative regulation of stem cell differentiation / regulation of epithelial cell proliferation / aortic valve morphogenesis / Notch binding / myoblast differentiation / RUNX3 regulates NOTCH signaling / negative regulation of fat cell differentiation / negative regulation of cell-matrix adhesion / positive regulation of Notch signaling pathway / negative regulation of cell-cell adhesion / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of neuron differentiation / RAC3 GTPase cycle / blood vessel remodeling / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / RAC1 GTPase cycle / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cell migration / NOTCH3 Activation and Transmission of Signal to the Nucleus / phospholipid binding / adherens junction / growth factor activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nervous system development / regulation of cell population proliferation / angiogenesis / molecular adaptor activity / apical plasma membrane / calcium ion binding / structural molecule activity / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / plasma membrane
Similarity search - Function
Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / von Willebrand factor (vWF) type C domain / EGF-like, conserved site ...Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / von Willebrand factor (vWF) type C domain / EGF-like, conserved site / Human growth factor-like EGF / von Willebrand factor (vWF) type C domain / VWFC domain / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsPayandeh, J. / de Leon-Boenig, G.
CitationJournal: Nature / Year: 2015
Title: Therapeutic antibodies reveal Notch control of transdifferentiation in the adult lung.
Authors: Lafkas, D. / Shelton, A. / Chiu, C. / de Leon Boenig, G. / Chen, Y. / Stawicki, S.S. / Siltanen, C. / Reichelt, M. / Zhou, M. / Wu, X. / Eastham-Anderson, J. / Moore, H. / Roose-Girma, M. / ...Authors: Lafkas, D. / Shelton, A. / Chiu, C. / de Leon Boenig, G. / Chen, Y. / Stawicki, S.S. / Siltanen, C. / Reichelt, M. / Zhou, M. / Wu, X. / Eastham-Anderson, J. / Moore, H. / Roose-Girma, M. / Chinn, Y. / Hang, J.Q. / Warming, S. / Egen, J. / Lee, W.P. / Austin, C. / Wu, Y. / Payandeh, J. / Lowe, J.B. / Siebel, C.W.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein jagged-1
B: Protein jagged-1
H: Fab heavy chain
I: Fab heavy chain
L: Fab light chain
M: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2738
Polymers126,0896
Non-polymers1842
Water2,846158
1
A: Protein jagged-1
I: Fab heavy chain
M: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1364
Polymers63,0443
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-38 kcal/mol
Surface area27500 Å2
MethodPISA
2
B: Protein jagged-1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1364
Polymers63,0443
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-38 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.258, 80.978, 155.616
Angle α, β, γ (deg.)90.00, 94.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein jagged-1 / hJ1


Mass: 16711.746 Da / Num. of mol.: 2 / Fragment: UNP residues 186-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAG1, JAGL1 / Plasmid: pAcGP67A / Details (production host): modified pAcGP67A / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P78504
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 22990.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 23341.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered antibody / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100 mM CHES pH 9.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.56→71.79 Å / Num. obs: 41207 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 59.89 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.4
Reflection shellResolution: 2.56→2.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Aimlessdata scaling
PHENIXphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VJ2, 2R0L

2vj2

2r0l


Resolution: 2.56→71.79 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.86 / SU R Cruickshank DPI: 0.72 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.668 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2075 5.04 %RANDOM
Rwork0.22 ---
obs0.222 41207 96.4 %-
Displacement parametersBiso mean: 41.55 Å2
Baniso -1Baniso -2Baniso -3
1-3.4702 Å20 Å21.5005 Å2
2--1.0991 Å20 Å2
3----4.5693 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: LAST / Resolution: 2.56→71.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 12 158 8916
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079007HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0612261HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2929SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes200HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1320HARMONIC5
X-RAY DIFFRACTIONt_it9007HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1161SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9818SEMIHARMONIC4
LS refinement shellResolution: 2.56→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2792 155 5.06 %
Rwork0.2275 2911 -
all0.2302 3066 -
obs--96.36 %

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