[English] 日本語
Yorodumi
- PDB-5bo1: Crystal structure of a human Jag1 fragment in complex with an ant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bo1
TitleCrystal structure of a human Jag1 fragment in complex with an anti-Jag1 Fab
Components
  • Fab heavy chain
  • Fab light chain
  • 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 / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / nephron development / morphogenesis of an epithelial sheet / Nephron development / pulmonary artery morphogenesis ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / nephron development / morphogenesis of an epithelial sheet / Nephron development / pulmonary artery morphogenesis / cardiac right ventricle morphogenesis / distal tubule development / inhibition of neuroepithelial cell differentiation / neuroendocrine cell differentiation / positive regulation of myeloid 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 / inner ear auditory receptor cell differentiation / endothelial cell differentiation / neuronal stem cell population maintenance / NOTCH4 Activation and Transmission of Signal to the Nucleus / pulmonary valve morphogenesis / cell fate determination / negative regulation of stem cell differentiation / regulation of epithelial cell proliferation / myoblast differentiation / aortic valve morphogenesis / Notch binding / RUNX3 regulates NOTCH signaling / negative regulation of cell-cell adhesion / negative regulation of neuron differentiation / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of cell-matrix adhesion / blood vessel remodeling / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / keratinocyte differentiation / Activated NOTCH1 Transmits Signal to the Nucleus / Notch signaling pathway / RAC1 GTPase cycle / NOTCH3 Activation and Transmission of Signal to the Nucleus / negative regulation of cell migration / adherens junction / growth factor activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / phospholipid binding / 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
: / Protein jagged-1-like, predicted ferredoxin-like domain / Jagged/Serrate protein / 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 / Delta-like/Jagged, EGF-like domain ...: / Protein jagged-1-like, predicted ferredoxin-like domain / Jagged/Serrate protein / 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 / Delta-like/Jagged, EGF-like domain / Teneurin EGF domain / EGF-like, conserved site / Human growth factor-like EGF / von Willebrand factor (vWF) type C domain / von Willebrand factor (vWF) type C domain / VWFC domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 1. / EGF-like domain signature 2. / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more