[English] 日本語
Yorodumi
- PDB-1bnd: STRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bnd
TitleSTRUCTURE OF THE BRAIN-DERIVED NEUROTROPHIC FACTOR(SLASH)NEUROTROPHIN 3 HETERODIMER
Components
  • BRAIN DERIVED NEUROTROPHIC FACTOR
  • NEUROTROPHIN 3
KeywordsCOMPLEX (GROWTH FACTOR/GROWTH FACTOR) / NEUROTROPHIN / COMPLEX (GROWTH FACTOR-GROWTH FACTOR) COMPLEX
Function / homology
Function and homology information


positive regulation of brain-derived neurotrophic factor receptor signaling pathway / NTF3 activates NTRK3 signaling / BDNF activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands ...positive regulation of brain-derived neurotrophic factor receptor signaling pathway / NTF3 activates NTRK3 signaling / BDNF activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / Activated NTRK3 signals through PLCG1 / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / Signaling by NTRK3 (TRKC) / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of myotube differentiation / Activated NTRK2 signals through CDK5 / nerve growth factor signaling pathway / NTRK2 activates RAC1 / collateral sprouting / regulation of protein localization to cell surface / Activated NTRK2 signals through FYN / nerve development / positive regulation of collateral sprouting / induction of positive chemotaxis / peripheral nervous system development / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K / activation of GTPase activity / positive regulation of synapse assembly / regulation of neuron differentiation / chemoattractant activity / negative regulation of apoptotic signaling pathway / positive regulation of receptor internalization / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Activated NTRK2 signals through FRS2 and FRS3 / synapse assembly / NPAS4 regulates expression of target genes / activation of protein kinase B activity / neuron projection morphogenesis / positive regulation of receptor binding / axon guidance / growth factor activity / modulation of chemical synaptic transmission / positive regulation of MAP kinase activity / positive regulation of neuron projection development / memory / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / synaptic vesicle / cell-cell signaling / positive regulation of peptidyl-serine phosphorylation / nervous system development / regulation of apoptotic process / negative regulation of neuron apoptotic process / positive regulation of cell migration / axon / endoplasmic reticulum lumen / signaling receptor binding / dendrite / positive regulation of cell population proliferation / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Brain-derived neurotrophic factor / Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. ...Brain-derived neurotrophic factor / Neurotrophin-3 / Neutrophin-3, N-terminal / Neutrophin-3 N-terminus / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like / Nerve growth factor family / Nerve growth factor family signature. / Nerve growth factor (NGF or beta-NGF) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Neurotrophin-3 / Brain-derived neurotrophic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRobinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure of the brain-derived neurotrophic factor/neurotrophin 3 heterodimer.
Authors: Robinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y.
#1: Journal: Biochemistry / Year: 1993
Title: Heterodimers of the Neurotrophic Factors: Formation, Isolation, and Differential Stability
Authors: Radziejewski, C. / Robinson, R.C.
History
DepositionDec 12, 1994Processing site: BNL
Revision 1.0Apr 4, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2513
Polymers27,1912
Non-polymers601
Water1,26170
1
A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules

A: BRAIN DERIVED NEUROTROPHIC FACTOR
B: NEUROTROPHIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5026
Polymers54,3824
Non-polymers1202
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-16 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.400, 45.100, 68.000
Angle α, β, γ (deg.)90.00, 118.30, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO B 47

-
Components

#1: Protein BRAIN DERIVED NEUROTROPHIC FACTOR / BDNF


Mass: 13534.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARM.; / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P23560
#2: Protein NEUROTROPHIN 3 / / NT3


Mass: 13656.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HETERODIMER / Source: (gene. exp.) Homo sapiens (human) / Description: SUPPLIED BY REGENERON PHARM.; / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P20783
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 %(w/v)PEG40001reservoir
310 %(v/v)2-propanol1reservoir
40.1 Msodium citrate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 11771 / % possible obs: 93.4 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 11691 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / % possible obs: 85.6 % / Num. unique obs: 1455 / Rmerge(I) obs: 0.15

-
Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→20 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 11691
Displacement parametersBiso mean: 45.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 4 70 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.354.35
X-RAY DIFFRACTIONx_mcangle_it6.656.65
X-RAY DIFFRACTIONx_scbond_it4.354.35
X-RAY DIFFRACTIONx_scangle_it6.656.65
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / Total num. of bins used: 9 / Num. reflection obs: 1455 / Rfactor all: 0.324

+
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