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- PDB-5cus: Crystal Structure of sErbB3-Fab3379 Complex -

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Basic information

Entry
Database: PDB / ID: 5cus
TitleCrystal Structure of sErbB3-Fab3379 Complex
Components
  • Fab LC region of KTN3379
  • IgG H chain
  • Receptor tyrosine-protein kinase erbB-3
KeywordsTRANSFERASE / ErbB3 / Antibody
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / negative regulation of signal transduction / Schwann cell development / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / immunoglobulin complex, circulating / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / basal plasma membrane / complement activation, classical pathway / antigen binding / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / antibacterial humoral response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / blood microparticle / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-3 / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLee, S. / Schlessinger, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Inhibition of ErbB3 by a monoclonal antibody that locks the extracellular domain in an inactive configuration.
Authors: Lee, S. / Greenlee, E.B. / Amick, J.R. / Ligon, G.F. / Lillquist, J.S. / Natoli, E.J. / Hadari, Y. / Alvarado, D. / Schlessinger, J.
History
DepositionJul 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list ...citation / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-3
B: Receptor tyrosine-protein kinase erbB-3
C: Receptor tyrosine-protein kinase erbB-3
D: Receptor tyrosine-protein kinase erbB-3
H: IgG H chain
L: Fab LC region of KTN3379
I: IgG H chain
J: IgG H chain
K: IgG H chain
M: Fab LC region of KTN3379
N: Fab LC region of KTN3379
O: Fab LC region of KTN3379
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,64023
Polymers461,20712
Non-polymers2,43311
Water00
1
A: Receptor tyrosine-protein kinase erbB-3
H: IgG H chain
L: Fab LC region of KTN3379
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7445
Polymers115,3023
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor tyrosine-protein kinase erbB-3
I: IgG H chain
M: Fab LC region of KTN3379
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9656
Polymers115,3023
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Receptor tyrosine-protein kinase erbB-3
J: IgG H chain
N: Fab LC region of KTN3379
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9656
Polymers115,3023
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Receptor tyrosine-protein kinase erbB-3
K: IgG H chain
O: Fab LC region of KTN3379
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9656
Polymers115,3023
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.378, 127.141, 138.078
Angle α, β, γ (deg.)87.100, 85.540, 89.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 69219.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P21860, receptor protein-tyrosine kinase
#2: Antibody
IgG H chain


Mass: 23351.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S6B291
#3: Antibody
Fab LC region of KTN3379


Mass: 22731.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: 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.: 11
Source method: isolated from a genetically manipulated source
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium Citrate, Sodium Thiocyanate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→69.39 Å / Num. obs: 92683 / % possible obs: 98.31 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.1015 / Net I/σ(I): 7.45
Reflection shellResolution: 3.2→3.314 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3211 / Mean I/σ(I) obs: 2.62 / % possible all: 98.25

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEO and 3H42

4leo

3h42


Resolution: 3.2→69.39 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 4593 4.96 %
Rwork0.2523 88078 -
obs0.2535 92671 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.06 Å2 / Biso mean: 67.7582 Å2 / Biso min: 6.12 Å2
Refinement stepCycle: final / Resolution: 3.2→69.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25742 0 154 0 25896
Biso mean--52.34 --
Num. residues----3642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226569
X-RAY DIFFRACTIONf_angle_d0.56836152
X-RAY DIFFRACTIONf_chiral_restr0.0224174
X-RAY DIFFRACTIONf_plane_restr0.0044724
X-RAY DIFFRACTIONf_dihedral_angle_d9.2388898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.23640.36841540.33162963311798
3.2364-3.27440.33881440.31882909305398
3.2744-3.31440.34781630.3032928309198
3.3144-3.35630.33691380.28712982312098
3.3563-3.40050.30571670.28932911307898
3.4005-3.44710.28941570.29022886304398
3.4471-3.49630.33071640.28092937310198
3.4963-3.54850.29171370.27482951308898
3.5485-3.60390.2681480.2682871301998
3.6039-3.6630.33591470.27682969311698
3.663-3.72620.30051440.26162937308198
3.7262-3.79390.26951410.25562914305598
3.7939-3.86690.25881480.25922931307998
3.8669-3.94580.26781560.25562911306798
3.9458-4.03160.25211490.24592943309298
4.0316-4.12540.26751730.23662911308498
4.1254-4.22850.23171680.23642936310498
4.2285-4.34290.25921700.22612872304298
4.3429-4.47060.23661090.21713003311298
4.4706-4.61490.24841180.22332935305398
4.6149-4.77980.25071610.21672949311098
4.7798-4.97110.29391530.21672932308598
4.9711-5.19730.25281680.21682892306098
5.1973-5.47120.25471750.22792924309998
5.4712-5.81380.26321560.24642962311899
5.8138-6.26250.27461920.25922905309799
6.2625-6.89220.27491260.26533030315699
6.8922-7.88830.30331740.26572950312499
7.8883-9.93370.23161560.24582953310999
9.9337-69.40650.31551370.25932981311899

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