[English] 日本語
Yorodumi
- PDB-5fiq: Exonuclease domain-containing 1 (Exd1) in the native conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fiq
TitleExonuclease domain-containing 1 (Exd1) in the native conformation
ComponentsEXD1
KeywordsHYDROLASE / EXONUCLEASE / PIRNA BIOGENESIS / DIMER / RNA BINDING
Function / homology
Function and homology information


PET complex / piRNA processing / P granule / regulatory ncRNA-mediated gene silencing / meiotic cell cycle / protein homodimerization activity / RNA binding
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
piRNA biogenesis protein EXD1
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / McCarthy, A.A. / Pillai, R.S.
CitationJournal: Mol.Cell / Year: 2016
Title: Piwi Slicing and Exd1 Drive Biogenesis of Nuclear Pirnas from Cytosolic Targets of the Mouse Pirna Pathway
Authors: Yang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / Mccarthy, A.A. / Pillai, R.S.
History
DepositionOct 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXD1
C: EXD1
E: EXD1
G: EXD1
I: EXD1


Theoretical massNumber of molelcules
Total (without water)140,5125
Polymers140,5125
Non-polymers00
Water95553
1
A: EXD1

A: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5290 Å2
ΔGint-32.1 kcal/mol
Surface area22810 Å2
MethodPISA
2
C: EXD1
E: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29.8 kcal/mol
Surface area22900 Å2
MethodPISA
3
G: EXD1
I: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-29.3 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.540, 81.580, 154.750
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15C
25E
16C
26G
17C
27I
18E
28G
19E
29I
110G
210I

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA75 - 3133 - 241
21ILEILECB75 - 3133 - 241
12ILEILEAA75 - 3133 - 241
22ILEILEEC75 - 3133 - 241
13ILEILEAA75 - 3133 - 241
23ILEILEGD75 - 3133 - 241
14ILEILEAA75 - 3133 - 241
24ILEILEIE75 - 3133 - 241
15ASPASPCB75 - 3143 - 242
25ASPASPEC75 - 3143 - 242
16ASPASPCB75 - 3143 - 242
26ASPASPGD75 - 3143 - 242
17ASPASPCB75 - 3143 - 242
27ASPASPIE75 - 3143 - 242
18ASPASPEC75 - 3143 - 242
28ASPASPGD75 - 3143 - 242
19ASPASPEC75 - 3143 - 242
29ASPASPIE75 - 3143 - 242
110ASPASPGD75 - 3143 - 242
210ASPASPIE75 - 3143 - 242

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(0.408, 0.884, -0.23), (-0.884, 0.32, -0.341), (-0.228, 0.342, 0.911)25.29546, -10.95703, -23.40071
2given(-0.405, -0.883, 0.236), (-0.885, 0.314, -0.344), (0.229, -0.349, -0.909)-81.69623, -10.76337, 167.43901
3given(-0.57, 0.549, -0.611), (-0.558, -0.805, -0.203), (-0.603, 0.226, 0.765)88.85638, -28.88748, -7.94666
4given(0.574, -0.542, 0.613), (-0.545, -0.812, -0.207), (0.61, -0.215, -0.762)-144.68066, -28.84359, 152.25386

-
Components

#1: Protein
EXD1


Mass: 28102.447 Da / Num. of mol.: 5 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 73-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Cell line: BMN4 / Organ: OVARIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: H9IUR0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN SEQUENCE CORRESPONDS TO MRNA SEQUENCE: GENBANK ID AK383154

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Description: OSCILLATION DATA WERE COLLECTED USING MXCUBEV2.0
Crystal growpH: 8.5
Details: 35% (W/V) 1,6-HEXANEDIOL, 50 MM TRIS-HCL PH 8.5, 5 MM MGSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 53690 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.3 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FIS

5fis


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 26.969 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24717 2596 4.8 %RANDOM
Rwork0.221 ---
obs0.22226 51094 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.51 Å2
2---3.16 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9685 0 0 53 9738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199855
X-RAY DIFFRACTIONr_bond_other_d0.010.029623
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.96213261
X-RAY DIFFRACTIONr_angle_other_deg1.569322224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50251197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26225.532470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.378151918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1151535
X-RAY DIFFRACTIONr_chiral_restr0.1130.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211019
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022192
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_it1.6592.0644803
X-RAY DIFFRACTIONr_mcbond_other1.6582.0634802
X-RAY DIFFRACTIONr_mcangle_it2.823.0865995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1062.3425051
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A299240.06
12C299240.06
21A299620.06
22E299620.06
31A299660.07
32G299660.07
41A297840.07
42I297840.07
51C298520.07
52E298520.07
61C298540.07
62G298540.07
71C297460.08
72I297460.08
81E297620.07
82G297620.07
91E299120.07
92I299120.07
101G299540.06
102I299540.06
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 148 -
Rwork0.326 3315 -
obs--83.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.30260.0292-0.56170.36340.1630.61830.01440.0502-0.0467-0.08330.0114-0.09270.08720.0377-0.02580.24680.01780.0970.75380.00260.0606-15.924-29.02462.979
20.7590.4436-0.80671.157-0.35711.1320.10550.02910.14190.0370.0816-0.0411-0.05470.1693-0.18710.2027-0.00740.1010.8386-0.03010.0847-20.536-12.62694.348
30.46390.2596-0.46210.9152-0.04681.3969-0.0795-0.1926-0.01280.21950.07650.01720.25820.03660.0030.30110.01850.08550.83040.02210.0348-34.453-27.405116.745
40.9143-0.2341-0.06860.5176-0.44172.60720.01950.02930.1729-0.14090.1107-0.1162-0.1444-0.2366-0.13020.2759-0.02720.13290.8245-0.00150.095417.044-41.432118.309
50.5389-0.2083-0.45480.53660.18042.7222-0.046-0.33940.14590.11910.0766-0.01590.34390.2468-0.03060.28150.03340.08620.9692-0.05250.076319.599-50.492147.005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A73 - 314
2X-RAY DIFFRACTION2C75 - 314
3X-RAY DIFFRACTION3E75 - 314
4X-RAY DIFFRACTION4G75 - 314
5X-RAY DIFFRACTION5I75 - 314

+
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