[English] 日本語
Yorodumi
- PDB-1sg1: Crystal Structure of the Receptor-Ligand Complex between Nerve Gr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sg1
TitleCrystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the Common Neurotrophin Receptor p75
Components
  • Beta-nerve growth factor
  • Tumor necrosis factor receptor superfamily member 16
KeywordsHORMONE/GROWTH FACTOR/MEMBRANE PROTEIN / Nerve Growth Factor / NGF / p75 / Neurotrophin / common neurotrophin receptor / growth factor receptor / receptor-ligand complex / HORMONE-GROWTH FACTOR-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NFG and proNGF binds to p75NTR / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NFG and proNGF binds to p75NTR / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / Ceramide signalling / death receptor activity / nerve growth factor receptor binding / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / NGF processing / positive regulation of synaptic transmission, cholinergic / TRKA activation by NGF / negative regulation of fibroblast growth factor receptor signaling pathway / PLC-gamma1 signalling / Signalling to STAT3 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / p75NTR negatively regulates cell cycle via SC1 / neurotrophin binding / negative regulation of dendritic spine development / metalloendopeptidase inhibitor activity / positive regulation of myelination / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / clathrin-coated endocytic vesicle / positive regulation of collateral sprouting / nerve growth factor binding / NADE modulates death signalling / Signalling to p38 via RIT and RIN / peripheral nervous system development / neurotrophin TRKA receptor binding / ARMS-mediated activation / positive regulation of neural precursor cell proliferation / positive regulation of Ras protein signal transduction / regulation of reactive oxygen species metabolic process / negative regulation of mitochondrial depolarization / PI3K/AKT activation / skin development / regulation of neuron differentiation / hair follicle morphogenesis / positive regulation of Rho protein signal transduction / Frs2-mediated activation / neuronal cell body membrane / NRAGE signals death through JNK / skeletal muscle cell differentiation / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / positive regulation of excitatory postsynaptic potential / Rho protein signal transduction / extrinsic apoptotic signaling pathway via death domain receptors / hair follicle development / Signalling to RAS / fibroblast growth factor receptor signaling pathway / positive regulation of DNA binding / coreceptor activity / dendrite membrane / p75NTR recruits signalling complexes / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / negative regulation of angiogenesis / positive regulation of synaptic transmission, glutamatergic / negative regulation of cell migration / neuron projection morphogenesis / central nervous system development / positive regulation of apoptotic signaling pathway / endosome lumen / cell surface receptor protein tyrosine kinase signaling pathway / axon guidance / intracellular protein transport / growth factor activity / circadian regulation of gene expression / modulation of chemical synaptic transmission / neuromuscular junction / memory / small GTPase binding / positive regulation of neuron projection development / positive regulation of miRNA transcription / Golgi lumen / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / positive regulation of fibroblast proliferation / cell-cell junction / synaptic vesicle / presynapse / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron projection development / glucose homeostasis / presynaptic membrane
Similarity search - Function
Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Nerve growth factor, beta subunit, mammalian / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor, beta subunit / Nerve growth factor family profile. / Nerve growth factor-related / Nerve growth factor conserved site / Nerve growth factor-like ...Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Nerve growth factor, beta subunit, mammalian / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / Nerve growth factor, beta subunit / 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) / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Cystine-knot cytokine / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-nerve growth factor / Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsHe, X.L. / Garcia, K.C.
CitationJournal: Science / Year: 2004
Title: Structure of nerve growth factor complexed with the shared neurotrophin receptor p75
Authors: He, X.L. / Garcia, K.C.
History
DepositionFeb 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-nerve growth factor
B: Beta-nerve growth factor
X: Tumor necrosis factor receptor superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3244
Polymers44,2893
Non-polymers351
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-30 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.692, 91.796, 92.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-nerve growth factor / Beta-NGF


Mass: 13515.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01138
#2: Protein Tumor necrosis factor receptor superfamily member 16 / Low- affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity ...Low- affinity nerve growth factor receptor / NGF receptor / Gp80-LNGFR / p75 ICD / Low affinity neurotrophin receptor p75NTR


Mass: 17258.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: p75 / Plasmid: pAcGP67A / Production host: unidentified baculovirus / Strain (production host): Tn5 / References: UniProt: P07174
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 1000, isoproponal, sodium chloride, citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0597 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2003 / Details: null
RadiationMonochromator: null / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 16891 / Num. obs: 16891 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.4 / % possible all: 97.3

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR
Starting model: part of the structure starts from PDB ENTRY 1WWW

1www


Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 803 -RANDOM
Rwork0.243 ---
all0.245 16891 --
obs0.245 16891 99 %-
Displacement parametersBiso mean: 50.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 1 375 3139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.411 85 -
Rwork0.4 --
obs-1648 97.3 %

+
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