[English] 日本語
Yorodumi
- PDB-4b36: Crystal Structure of Human Angiogenin with an Engineered Loop Exh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b36
TitleCrystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule
ComponentsANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN
KeywordsHYDROLASE / EDN / ANG / ANTIVIRAL / ANGIOGENESIS / TUMOR / AMYOTROPHIC LATERAL SCLEROSIS / PARKINSONS DISEASE
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 / homeostatic process ...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 / 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 / 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
Angiogenin / Eosinophil cationic-related protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsThiyagarajan, N. / Acharya, K.R.
CitationJournal: FEBS Open Bio. / Year: 2012
Title: Crystal Structure of Human Angiogenin with an Engineered Loop Exhibits Conformational Flexibility at the Functional Regions of the Molecule
Authors: Thiyagarajan, N. / Acharya, K.R.
History
DepositionJul 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN
B: ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1184
Polymers29,0472
Non-polymers712
Water1,53185
1
A: ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,5231
Polymers14,5231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5943
Polymers14,5231
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.353, 54.676, 94.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ANGIOGENIN, EOSINOPHIL CATIONIC-RELATED PROTEIN / / RIBONUCLEASE 5 / RNASE 5 / ANGIOGENIN-EOSINOPHIL DERIVED NEUROTOXIN HYBRID


Mass: 14523.436 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-107,111-120,116-147
Source method: isolated from a genetically manipulated source
Details: IN THIS STUDY WE HAVE SUBSTITUTED 84- HGGSPWPP-91 OF ANG WITH 86-TTPSPQNISN-95 OF EOSINOPHIL- DERIVED NEUROTOXIN AND CONSTRUCTED AN ANG-EDN HYBRID
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIPL
References: UniProt: P03950, UniProt: Q12762, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THIS STUDY WE HAVE SUBSTITUTED 84-HGGSPWPP-91 OF ANG WITH 86-TTPSPQNISN-95 OF EOSINOPHIL-DERIVED ...IN THIS STUDY WE HAVE SUBSTITUTED 84-HGGSPWPP-91 OF ANG WITH 86-TTPSPQNISN-95 OF EOSINOPHIL-DERIVED NEUROTOXIN AND CONSTRUCTED AN ANG-EDN HYBRID

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.2 % / Description: NONE
Crystal growDetails: 1.75-2.5 M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 20481 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 27.12 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / % possible all: 65.8

-
Processing

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

1ang


Resolution: 1.76→20.151 Å / SU ML: 0.18 / σ(F): 0.1 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 933 5.1 %
Rwork0.2365 --
obs0.2389 18214 89.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.578 Å2 / ksol: 0.427 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8845 Å20 Å20 Å2
2---8.3103 Å20 Å2
3---3.4258 Å2
Refinement stepCycle: LAST / Resolution: 1.76→20.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 2 85 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071859
X-RAY DIFFRACTIONf_angle_d1.0122495
X-RAY DIFFRACTIONf_dihedral_angle_d13.283704
X-RAY DIFFRACTIONf_chiral_restr0.067273
X-RAY DIFFRACTIONf_plane_restr0.006328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7601-1.85290.3677910.25751776X-RAY DIFFRACTION66
1.8529-1.96890.31751360.2352515X-RAY DIFFRACTION92
1.9689-2.12070.26111620.21312634X-RAY DIFFRACTION97
2.1207-2.33390.32881510.21722652X-RAY DIFFRACTION98
2.3339-2.67090.30211580.2452687X-RAY DIFFRACTION97
2.6709-3.36250.31341230.23472620X-RAY DIFFRACTION94
3.3625-20.15190.23491120.23872397X-RAY DIFFRACTION81

+
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