[English] 日本語
Yorodumi
- PDB-5m9v: Human angiogenin PD/ALS variant R121C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m9v
TitleHuman angiogenin PD/ALS variant R121C
ComponentsAngiogenin
KeywordsHYDROLASE / Parkinson's / RNase / angiogenesis / ALS
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 / peptide binding / RNA endonuclease activity / stress granule assembly / 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 / angiogenesis / endonuclease activity / 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 / cytosol / cytoplasm
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
GLUTATHIONE / L(+)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBradshaw, W.J. / Rehman, S. / Pham, T.T.K. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust083191 United Kingdom
Wellcome Trust088464 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into human angiogenin variants implicated in Parkinson's disease and Amyotrophic Lateral Sclerosis.
Authors: Bradshaw, W.J. / Rehman, S. / Pham, T.T. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
History
DepositionNov 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7043
Polymers14,2461
Non-polymers4572
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint0 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.539, 118.969, 37.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-506-

HOH

-
Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14246.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C121 is has a glutathione bound, for refinement purposes this was modelled as a cysteine in the same chain, which has been added to the alignment.
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GSH / GLUTATHIONE / Ribonuclease 5 / RNase 5


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
Details: C121 is has a glutathione bound, for refinement purposes this was modelled as a cysteine in the same chain, which has been added to the alignment.
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Na/K tartrate 0.1 M bis-tris propane 16% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→67.8 Å / Num. obs: 20751 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.997 / Net I/σ(I): 7.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 1063 / CC1/2: 0.47 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANG

1ang


Resolution: 1.7→67.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.658 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23883 1054 5.1 %RANDOM
Rwork0.20873 ---
obs0.21025 19631 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.177 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2--3.26 Å20 Å2
3----2.18 Å2
Refinement stepCycle: 1 / Resolution: 1.7→67.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 10 110 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191066
X-RAY DIFFRACTIONr_bond_other_d0.0010.02978
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9321442
X-RAY DIFFRACTIONr_angle_other_deg0.97432250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32622.556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27715178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4981513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0442.948516
X-RAY DIFFRACTIONr_mcbond_other2.0432.942515
X-RAY DIFFRACTIONr_mcangle_it3.3444.393646
X-RAY DIFFRACTIONr_mcangle_other3.3424.402647
X-RAY DIFFRACTIONr_scbond_it2.5653.296549
X-RAY DIFFRACTIONr_scbond_other2.5623.296546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3254.808793
X-RAY DIFFRACTIONr_long_range_B_refined7.06435.4951184
X-RAY DIFFRACTIONr_long_range_B_other6.8834.5111146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 76 -
Rwork0.375 1413 -
obs--99.93 %

+
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