[English] 日本語
Yorodumi
- PDB-7bhf: DARPin_D5/Her3 domain 4 complex, orthorhombic crystals -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bhf
TitleDARPin_D5/Her3 domain 4 complex, orthorhombic crystals
Components
  • DARPin_D5
  • Isoform 4 of Receptor tyrosine-protein kinase erbB-3
KeywordsPROTEIN BINDING / designed ankyrin repeat protein
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 / 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 / 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 / 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 / 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 / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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 ...Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.997 Å
AuthorsMittl, P.R.E. / Radom, F. / Pluckthun, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5.
Authors: Radom, F. / Vonrhein, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DARPin_D5
B: Isoform 4 of Receptor tyrosine-protein kinase erbB-3
C: DARPin_D5
D: Isoform 4 of Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2156
Polymers62,0974
Non-polymers1182
Water12,430690
1
A: DARPin_D5
B: Isoform 4 of Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1083
Polymers31,0492
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-10 kcal/mol
Surface area12980 Å2
MethodPISA
2
C: DARPin_D5
D: Isoform 4 of Receptor tyrosine-protein kinase erbB-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1083
Polymers31,0492
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.258, 64.951, 144.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DARPin_D5


Mass: 14908.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Isoform 4 of Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 16140.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.74 / Details: 0.1 M Na citrate, 10% PEG4000, 0.2 M Li sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.997→38.192 Å / Num. obs: 38572 / % possible obs: 94.7 % / Redundancy: 8.87 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.075 / Rrim(I) all: 0.23 / Net I/σ(I): 7.4
Reflection shellResolution: 1.997→2.031 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.657 / Num. unique obs: 1904 / CC1/2: 0.387 / Rpim(I) all: 0.61 / Rrim(I) all: 1.776 / % possible all: 96.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.3 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BHE

7bhe


Resolution: 1.997→38.19 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 1841 4.78 %RANDOM
Rwork0.1981 ---
obs0.2003 38548 94.7 %-
Displacement parametersBiso max: 91.14 Å2 / Biso mean: 31.28 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1-4.0178 Å20 Å20 Å2
2--2.22 Å20 Å2
3----6.2378 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.997→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 8 690 4518
Biso mean--39.79 40.79 -
Num. residues----514
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1343SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it4010HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
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_contact4024SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4010HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5467HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion15.52
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2875 38 4.93 %
Rwork0.261 733 -
all0.2624 771 -
obs--92.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11850.54810.58481.02911.40713.7879-0.1634-0.0532-0.1142-0.05560.02960.0079-0.1232-0.05610.1338-0.13640.00410.0009-0.0685-0.02530.0539-6.805514.343735.8004
21.18390.81380.29163.11380.64361.452-0.04520.02560.0291-0.28970.0752-0.09710.0513-0.0204-0.03-0.1114-0.05040.0197-0.0338-0.0056-0.06091.0274.048116.012
32.08440.98030.84681.48461.80564.0361-0.13560.03580.076-0.00810.02180.0195-0.0543-0.00260.1139-0.14260.01310.0051-0.0699-0.04090.0624-6.825629.9999108.877
40.9506-0.12820.1661.793-0.18311.37770.0887-0.0118-0.0038-0.29480.0181-0.02510.089-0.0258-0.1068-0.0934-0.04680.0207-0.05390.0275-0.03311.084919.64988.3853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A11 - 136
2X-RAY DIFFRACTION2{ B|* }B481 - 611
3X-RAY DIFFRACTION3{ C|* }C11 - 136
4X-RAY DIFFRACTION4{ D|* }D481 - 611

+
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://pdbjlvh1.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