[English] 日本語
Yorodumi
- PDB-3u9u: Crystal Structure of Extracellular Domain of Human ErbB4/Her4 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u9u
TitleCrystal Structure of Extracellular Domain of Human ErbB4/Her4 in complex with the Fab fragment of mAb1479
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • Receptor tyrosine-protein kinase erbB-4
KeywordsTRANSFERASE / Cell Surface Receptor / Tyrosine Kinase Receptor
Function / homology
Function and homology information


establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding ...establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding / PI3K events in ERBB4 signaling / mammary gland epithelial cell differentiation / embryonic pattern specification / positive regulation of protein localization to cell surface / neurotransmitter receptor localization to postsynaptic specialization membrane / epidermal growth factor receptor activity / neural crest cell migration / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / PI3K events in ERBB2 signaling / GABA-ergic synapse / SHC1 events in ERBB4 signaling / mammary gland alveolus development / cell fate commitment / Nuclear signaling by ERBB4 / regulation of cell migration / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cardiac muscle cell proliferation / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / synapse assembly / Downregulation of ERBB4 signaling / lactation / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / neurogenesis / SHC1 events in ERBB2 signaling / basal plasma membrane / postsynaptic density membrane / Signaling by ERBB2 TMD/JMD mutants / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / presynaptic membrane / nervous system development / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / postsynaptic membrane / basolateral plasma membrane / protein tyrosine kinase activity / Estrogen-dependent gene expression / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / transcription cis-regulatory region binding / mitochondrial matrix / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe ...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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / 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 / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsHollmen, M. / Liu, P. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. ...Hollmen, M. / Liu, P. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. / Schoffski, P. / Elenius, K.
CitationJournal: Plos One / Year: 2012
Title: Proteolytic processing of ErbB4 in breast cancer.
Authors: Hollmen, M. / Liu, P. / Kurppa, K. / Wildiers, H. / Reinvall, I. / Vandorpe, T. / Smeets, A. / Deraedt, K. / Vahlberg, T. / Joensuu, H. / Leahy, D.J. / Schoffski, P. / Elenius, K.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab Heavy Chain
B: Fab Light Chain
C: Fab Heavy Chain
D: Fab Light Chain
E: Receptor tyrosine-protein kinase erbB-4
F: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)236,5376
Polymers236,5376
Non-polymers00
Water0
1
A: Fab Heavy Chain
B: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,4012
Polymers48,4012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-29 kcal/mol
Surface area19720 Å2
MethodPISA
2
C: Fab Heavy Chain
D: Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,4012
Polymers48,4012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-30 kcal/mol
Surface area19320 Å2
MethodPISA
3
E: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)69,8681
Polymers69,8681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)69,8681
Polymers69,8681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.121, 110.914, 362.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Fab Heavy Chain / Fragment antigen-binding


Mass: 24195.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Hybridoma Cells / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Mus musculus (house mouse)
#2: Antibody Fab Light Chain / Fragment antigen-binding


Mass: 24205.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Hybridoma Cells / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Mus musculus (house mouse)
#3: Protein Receptor tyrosine-protein kinase erbB-4 / Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 ...Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 / ERBB4 intracellular domain / 4ICD / E4ICD / s80HER4


Mass: 69867.766 Da / Num. of mol.: 2 / Fragment: Extracellular region 1-625, JM-a isoform
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: PSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO (Lec1)
References: UniProt: Q15303, receptor protein-tyrosine kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG4000, 0.2 M Sodium Acetate, 0.1 M Sodium Citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2010
RadiationMonochromator: Doulbe Crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 44255 / Num. obs: 44255 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 73.77 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.4-3.522.30.612195.8
3.52-3.662.50.502197.6
3.66-3.832.80.411197.9
3.83-4.032.90.317197.7
4.03-4.2830.229197.4
4.28-4.6130.154196.3
4.61-5.0830.118196.3
5.08-5.8130.113194.7
5.81-7.323.10.083193.3
7.32-5030.042186.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHX, 1N8Z

2ahx

1n8z


Resolution: 3.42→45.26 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.7841 / Occupancy max: 1 / Occupancy min: 0.51 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 2230 5.05 %RANDOM
Rwork0.2341 ---
obs0.236 44127 95.26 %-
all-44127 --
Displacement parametersBiso mean: 112.38 Å2
Baniso -1Baniso -2Baniso -3
1--64.2676 Å20 Å20 Å2
2--34.444 Å20 Å2
3---29.8236 Å2
Refine analyzeLuzzati coordinate error obs: 0.864 Å
Refinement stepCycle: LAST / Resolution: 3.42→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15819 0 0 0 15819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00916230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1622070HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5460SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes398HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2345HARMONIC5
X-RAY DIFFRACTIONt_it16230HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact
LS refinement shellResolution: 3.42→3.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2919 183 5.71 %
Rwork0.2574 3020 -
all0.2593 3203 -
obs--95.26 %
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)
10.1561-0.29990.19032.61870.90892.8439-0.013-0.04790.1494-0.19790.01560.03420.0547-0.0172-0.00260.1130.0157-0.0093-0.18260.0113-0.08-17.334517.623130.2094
20.4738-1.0522-0.83062.78551.37190.95830.0048-0.02420.126-0.03810.02280.19310.1433-0.0399-0.02750.0801-0.0034-0.1073-0.16760.00960.0724-28.83877.840739.6063
30.25240.2030.10473.1046-1.27920.6276-0.0215-0.03180.0356-0.05930.0260.1017-0.05110.0347-0.00450.01760.0325-0.0588-0.0857-0.02010.0061-18.2832-38.37542.5255
40.59320.6586-1.21141.0546-1.59382.06380.01160.00870.0048-0.13330.059-0.12180.06940.1023-0.07060.12970.0498-0.0177-0.115-0.0068-0.0491-6.2572-47.600432.8577
500.2844-0.09820.91551.03060.240.08190.0382-0.12790.1495-0.0013-0.0680.0955-0.0713-0.0806-0.15480.1469-0.00570.0584-0.08220.001121.2652-20.677.1798
60.2341-0.19010.49431.3479-1.1670.6544-0.02590.2634-0.0770.25820.02910.05360.0319-0.0686-0.00320.05140.0234-0.0071-0.0119-0.1085-0.1343-18.618-19.88-31.9436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|224 }A1 - 224
2X-RAY DIFFRACTION2{ B|1 - B|219 }B1 - 219
3X-RAY DIFFRACTION3{ C|1 - C|220 }C1 - 220
4X-RAY DIFFRACTION4{ D|1 - D|219 }D1 - 219
5X-RAY DIFFRACTION5{ E|2 - E|612 }E2 - 612
6X-RAY DIFFRACTION6{ F|2 - F|611 }F2 - 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://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