[English] 日本語
Yorodumi
- PDB-4aoh: Structural snapshots and functional analysis of human angiogenin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aoh
TitleStructural snapshots and functional analysis of human angiogenin variants associated with Amyotrophic Lateral Sclerosis (ALS)
ComponentsANGIOGENIN
KeywordsHYDROLASE / ANGIOGENESIS / NEOVASCULARISATION / AMYOTROPIC LATERAL SCLEROSIS / ALS / MOTOR NEURON DISEASE / RIBONUCLEASE INHIBITOR / NUCLEAR LOCALISATION / NUCLEAR LOCALIZATION
Function / homology
Function and homology information


angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation ...angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / positive regulation of phosphorylation / endocytic vesicle / RNA nuclease activity / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / peptide binding / RNA endonuclease activity / placenta development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cell migration / heparin binding / actin cytoskeleton / chromosome / ribosome binding / growth cone / actin binding / endonuclease activity / angiogenesis / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / receptor ligand activity / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / negative regulation of apoptotic process / nucleolus / signal transduction / protein homodimerization activity / extracellular space / DNA binding / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.041 Å
AuthorsThiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R.
CitationJournal: Nat.Commun. / Year: 2012
Title: Structural and Molecular Insights Into the Mechanism of Action of Human Angiogenin-Als Variants in Neurons
Authors: Thiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R.
History
DepositionMar 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...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 / 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5403
Polymers14,2401
Non-polymers3002
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.549, 37.505, 37.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

21A-2123-

HOH

-
Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14240.115 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS-RIPL
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growpH: 7
Details: 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 58714 / % possible obs: 82.7 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 11.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.1
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 37.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANG

1ang


Resolution: 1.041→42.774 Å / SU ML: 0.07 / σ(F): 1.35 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 2463 5.1 %
Rwork0.1689 --
obs0.1698 48524 82.69 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.701 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.0236 Å20 Å20 Å2
2---0.3581 Å20 Å2
3---0.3818 Å2
Refinement stepCycle: LAST / Resolution: 1.041→42.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 20 155 1155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061118
X-RAY DIFFRACTIONf_angle_d1.1361518
X-RAY DIFFRACTIONf_dihedral_angle_d11.001440
X-RAY DIFFRACTIONf_chiral_restr0.077158
X-RAY DIFFRACTIONf_plane_restr0.005207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0407-1.06070.3669540.3266916X-RAY DIFFRACTION31
1.0607-1.08240.2769550.24731447X-RAY DIFFRACTION47
1.0824-1.10590.2124890.20431721X-RAY DIFFRACTION56
1.1059-1.13170.20831260.15922008X-RAY DIFFRACTION66
1.1317-1.160.20381120.14382192X-RAY DIFFRACTION72
1.16-1.19130.14121280.14522383X-RAY DIFFRACTION78
1.1913-1.22640.16911310.14252626X-RAY DIFFRACTION85
1.2264-1.2660.16091530.14232747X-RAY DIFFRACTION90
1.266-1.31120.15941600.13562887X-RAY DIFFRACTION94
1.3112-1.36370.15841560.13142930X-RAY DIFFRACTION95
1.3637-1.42580.15281670.12772946X-RAY DIFFRACTION95
1.4258-1.5010.16481560.13122983X-RAY DIFFRACTION96
1.501-1.5950.16141460.13362960X-RAY DIFFRACTION97
1.595-1.71820.16511800.14353017X-RAY DIFFRACTION97
1.7182-1.89110.17951710.15363017X-RAY DIFFRACTION97
1.8911-2.16470.19811520.16723080X-RAY DIFFRACTION98
2.1647-2.72720.21371770.18323095X-RAY DIFFRACTION97
2.7272-42.81070.1931500.19493106X-RAY DIFFRACTION93

+
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