[English] 日本語
Yorodumi
- PDB-1he7: Human Nerve growth factor receptor TrkA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1he7
TitleHuman Nerve growth factor receptor TrkA
ComponentsHIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
KeywordsTRANSFERASE / TRK-RECEPTOR / STRAND-SWAPPING / NERVE GROWTH FACTOR
Function / homology
Function and homology information


behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / mechanoreceptor differentiation / neurotrophin receptor activity ...behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / mechanoreceptor differentiation / neurotrophin receptor activity / nerve growth factor receptor activity / neurotrophin binding / Sertoli cell development / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / axonogenesis involved in innervation / Retrograde neurotrophin signalling / nerve growth factor binding / NGF-independant TRKA activation / sympathetic nervous system development / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / response to axon injury / Signalling to RAS / neuron development / detection of mechanical stimulus involved in sensory perception of pain / peptidyl-tyrosine autophosphorylation / response to electrical stimulus / transmembrane receptor protein tyrosine kinase activity / B cell differentiation / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / positive regulation of GTPase activity / cellular response to nerve growth factor stimulus / axon guidance / receptor protein-tyrosine kinase / kinase binding / positive regulation of neuron projection development / cellular response to nicotine / peptidyl-tyrosine phosphorylation / circadian rhythm / positive regulation of angiogenesis / recycling endosome membrane / neuron projection development / late endosome / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / learning or memory / receptor complex / endosome membrane / positive regulation of protein phosphorylation / response to xenobiotic stimulus / protein phosphorylation / negative regulation of cell population proliferation / axon / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Leucine rich repeat / : / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBanfield, M. / Robertson, A. / Allen, S. / Dando, J. / Tyler, S. / Bennett, G. / Brain, S. / Mason, G. / Holden, P. / Clarke, A. ...Banfield, M. / Robertson, A. / Allen, S. / Dando, J. / Tyler, S. / Bennett, G. / Brain, S. / Mason, G. / Holden, P. / Clarke, A. / Naylor, R. / Wilcock, G. / Brady, R. / Dawbarn, D.
Citation
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of the Neurotrophin-Binding Domain of Trka, Trkb and Trkc
Authors: Ultsch, M.H. / Wiesmann, C. / Simmons, L.C. / Henrich, J. / Yang, M. / Reilly, D. / Bass, S.H. / De Vos, A.M.
#2: Journal: Nature / Year: 1999
Title: Crystal Structure of Nerve Growth Factor in Complex with the Ligand-Binding Domain of the Trka Receptor
Authors: Wiesmann, C. / Ultsch, M.H. / Bass, S.H. / De Vos, A.M.
History
DepositionNov 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2001Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0142
Polymers13,9221
Non-polymers921
Water57632
1
A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules

A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0294
Polymers27,8452
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area4770 Å2
ΔGint-42.2 kcal/mol
Surface area13900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)50.854, 50.854, 107.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

DetailsIN DILUTE SOLUTION THE PROTEIN EXISTS AS A MONOMER (NOSTRAND-SWAPPING) AND IS ACTIVE. THE PROTEIN IS INACTIVE INTHE DIMERIC FORM SEEN IN THE CRYSTAL. THE MATRICES FORCONTRUCTING THE DIMER ARE GIVEN IN REMARK 350 BELOW

-
Components

#1: Protein HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR / TRK1 TRANSFORMING TYROSINE KINASE PROTEIN / P140-TRKA / TRK-A


Mass: 13922.378 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, SPANS RESIDUES 285-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04629, EC: 2.7.1.112
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSTRUCTURE PRESENTED IS OF A STRAND-SWAPPED DIMER. THE SECOND MONOMER IS GENERATED THROUGH ...STRUCTURE PRESENTED IS OF A STRAND-SWAPPED DIMER. THE SECOND MONOMER IS GENERATED THROUGH CRYSTALLOGRAPHIC SYMMETRY. THIS IS NOT THE BIOLOGICALLY ACTIVE FORM OF THE MOLECULE. IT IS ACTIVE ONLY IN THE NON-STRAND SWAPPED STATE.
Has protein modificationY
Sequence detailsTHIS ENTRY IS A SPLICE VARIANT OF THE TRKA_HUMAN (P04629) SEQUENCE IN WHICH RESIDUES 393-398 ARE NOT PRESENT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 32.4 %
Crystal growpH: 4.7
Details: 10 MG/ML PROTEIN + 0.1-0.3M NACL, 0.1M NA-CITRATE, PH 4.6 - 4.8
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
20.1 %sodium azide11
35 mMBis-Tris11
4100-300 mM12NaCl
5100 mMNa citrate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 43.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WWA

1wwa


Resolution: 2→40 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FOLLOWING ATOMS WERE SET TO ZERO OCCUPANCY AS THEY WERE NOT OBSERVED IN ELECTRON DENSITY, SER A:304 ATOM: OG GLN A:308 ATOMS: CD OE1 NE2 GLU: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflection
Rfree0.276 992 10 %
Rwork0.237 --
obs0.237 10145 99.9 %
Solvent computationBsol: 46.8 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.987 Å20 Å20 Å2
2---8.987 Å20 Å2
3---17.974 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 6 32 876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.7562
X-RAY DIFFRACTIONc_scbond_it2.2382
X-RAY DIFFRACTIONc_scangle_it3.1522.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 123 10 %
Rwork0.254 1109 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3GOL.PAR
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

+
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