[English] 日本語
Yorodumi
- PDB-1gv7: ARH-I, an angiogenin/RNase A chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gv7
TitleARH-I, an angiogenin/RNase A chimera
ComponentsANGIOGENIN
KeywordsHYDROLASE / PANCREATIC RIBONUCLEASE / ANGIOGENESIS / ANGIOGENIN / CHIMERA / HYBRID / HOMOLOG SCANNING MUTAGENESIS
Function / homology
Function and homology information


activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / pancreatic ribonuclease ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / oocyte maturation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / pancreatic ribonuclease / ribonuclease A activity / homeostatic process / rRNA transcription / activation of phospholipase C activity / basement membrane / RNA nuclease activity / ovarian follicle development / positive regulation of phosphorylation / RNA endonuclease activity / actin filament polymerization / positive regulation of endothelial cell proliferation / activation of protein kinase B activity / response to hormone / placenta development / negative regulation of smooth muscle cell proliferation / positive regulation of protein secretion / peptide binding / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / heparin binding / chromosome / actin binding / antibacterial humoral response / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / nucleic acid binding / rRNA binding / response to hypoxia / lyase activity / defense response to Gram-positive bacterium / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / 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
CITRIC ACID / Ribonuclease pancreatic / Angiogenin / Ribonuclease pancreatic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHolloway, D.E. / Shapiro, R. / Hares, M.C. / Leonidas, D.D. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 2002
Title: Guest-Host Crosstalk in an Angiogenin-RNase A Chimeric Protein
Authors: Holloway, D.E. / Shapiro, R. / Hares, M.C. / Leonidas, D.D. / Acharya, K.R.
History
DepositionFeb 6, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2002Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow / pdbx_database_proc
Item: _citation.title / _exptl_crystal_grow.temp
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)14,1682
Polymers13,9761
Non-polymers1921
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.547, 64.199, 61.250
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-2002-

HOH

21A-2006-

HOH

-
Components

#1: Protein ANGIOGENIN /


Mass: 13975.849 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) BOS TAURUS (cattle)
Description: SUBSTITUTED SEQUENCE IS BOVINE. SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110
References: UniProt: P03950, UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSUBSTITUTION OF ANGIOGENIN RESIDUES 58-70 WITH RNASE A RESIDUES 85-97
Sequence detailsCHIMERA, DESCRIBED IN HARPER ET AL (1988) PNAS 85, 7139-43

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.8
Details: VAPOUR DIFFUSION, 16 C 10 MG/ML PROTEIN, 15 % PEG 4000, 8 % TERT-BUTANOL, 0.3 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE BUFFER, PH 5.8
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1droppH5.8
27.5 %(w/v)PEG40001drop
34 %(v/v)tert-butyl alcohol1drop
40.15 Mammonium acetate1drop
50.15 Msodium citrate1drop
615 %(w/v)PEG40001reservoir
78 %(v/v)tert-butyl alcohol1reservoir
80.3 Mammonium acetate1reservoir
90.1 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 8426 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2 / % possible all: 89.7
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 90 % / Num. measured all: 53460
Reflection shell
*PLUS
% possible obs: 89.7 % / Mean I/σ(I) obs: 2

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B1I

1b1i


Resolution: 2.1→22.88 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 837742.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 894 10.6 %RANDOM
Rwork0.22 ---
obs0.22 8425 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54 Å2 / ksol: 0.32194 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 13 62 1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 125 9.1 %
Rwork0.325 1251 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LPYGLU_PROSTHETIC.PARAMLPYGLU_PROSTHETIC.TOP
X-RAY DIFFRACTION4CITRATE_O_70.PARAMCITRATE_O_70.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 22.9 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

+
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