[English] 日本語
Yorodumi
- PDB-4wkj: Crystallographic Structure of a Dodecameric RNA-DNA Hybrid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wkj
TitleCrystallographic Structure of a Dodecameric RNA-DNA Hybrid
Components
  • DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
  • RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
KeywordsRNA/DNA / RNA / DNA / Hybrid / Duplex / RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDavis, R.R. / Shaban, N.M. / Perrino, F.W. / Hollis, T.
Funding support United States, 3items
OrganizationGrant numberCountry
American Heart Association10GRNT3650033 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069962 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108827 United States
CitationJournal: Cell Cycle / Year: 2015
Title: Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding.
Authors: Davis, R.R. / Shaban, N.M. / Perrino, F.W. / Hollis, T.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: pdbx_audit_support / pdbx_database_status ...pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible ..._pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
D: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
E: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
A: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
B: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
C: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
F: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
G: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
H: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9239
Polymers29,8998
Non-polymers241
Water181
1
D: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
E: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4752
Polymers7,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-7 kcal/mol
Surface area4460 Å2
MethodPISA
2
A: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
B: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4752
Polymers7,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-6 kcal/mol
Surface area4460 Å2
MethodPISA
3
C: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
F: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4993
Polymers7,4752
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area4520 Å2
MethodPISA
4
G: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
H: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4752
Polymers7,4752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-6 kcal/mol
Surface area4470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.649, 44.459, 83.346
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22C
13D
23G
14E
24B
15E
25F
16E
26H
17A
27C
18A
28G
19B
29F
110B
210H
111C
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _ / Auth seq-ID: 1 - 12 / Label seq-ID: 1 - 12

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-ID
11GGCCDA
21GGCCAC
12GGCCDA
22GGCCCE
13GGCCDA
23GGCCGG
14DGDGDCDCEB
24DGDGDCDCBD
15DGDGDCDCEB
25DGDGDCDCFF
16DGDGDCDCEB
26DGDGDCDCHH
17GGCCAC
27GGCCCE
18GGCCAC
28GGCCGG
19DGDGDCDCBD
29DGDGDCDCFF
110DGDGDCDCBD
210DGDGDCDCHH
111GGCCCE
211GGCCGG
112DGDGDCDCFF
212DGDGDCDCHH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: RNA chain
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')


Mass: 3772.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain
DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')


Mass: 3702.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M magnesium formate, 10% 2-Methyl-2,4-pentanediol
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryojet
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→26.27 Å / Num. obs: 8314 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 47.57 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0085refinement
Cootmodel building
CrystalCleardata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBI

1zbi


Resolution: 2.8→26.27 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.503 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24204 796 9.6 %RANDOM
Rwork0.23837 ---
obs0.23874 7484 99.53 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å20.04 Å2
2--1.83 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: 1 / Resolution: 2.8→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1980 1 1 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0112212
X-RAY DIFFRACTIONr_bond_other_d0.0120.021016
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.2253416
X-RAY DIFFRACTIONr_angle_other_deg2.22132432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021124
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02476
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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)
11D14140.01
12A14140.01
21D14040.03
22C14040.03
31D13880.04
32G13880.04
41E16620.05
42B16620.05
51E16360.08
52F16360.08
61E16360.07
62H16360.07
71A14080.03
72C14080.03
81A13960.04
82G13960.04
91B16520.06
92F16520.06
101B16560.05
102H16560.05
111C14120.03
112G14120.03
121F16380.08
122H16380.08
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 52 -
Rwork0.503 547 -
obs--99.5 %
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)
12.12680.682-2.3130.2603-0.792.5966-0.0731-0.0412-0.2201-0.0384-0.1298-0.0710.16370.15810.20290.3275-0.0626-0.03020.365-0.02090.369710.873-10.09910.59
23.19843.5677-0.62045.1641-1.32236.13670.2335-0.2150.2194-0.0559-0.59150.245-0.12960.34440.35790.2772-0.0927-0.00790.29540.04560.343512.65-6.93810.048
32.5842-0.1466-1.57120.05710.31352.1628-0.0415-0.2281-0.07480.039-0.04980.02070.3280.00380.09130.28380.1321-0.01360.27730.04890.365612.449-10.123-10.528
43.5341-3.6763-0.84964.09121.65533.79740.09050.1540.1116-0.0613-0.3451-0.1039-0.0712-0.33810.25470.28360.10940.00420.2903-0.03730.360910.713-6.994-9.975
54.2671-1.6539-1.85513.73181.32791.0590.0437-0.0886-0.08450.00610.14550.06050.02280.0138-0.18920.0440.0157-0.07060.0520.08190.40488.9975.85-35.799
61.4819-1.7806-1.63053.67971.12084.6971-0.1122-0.0852-0.43020.00350.27140.26540.0063-0.1032-0.15920.13480.03380.05550.05060.01060.44056.8247.233-33.432
75.2058-1.3206-1.33182.1890.63430.3904-0.2146-0.19620.0173-0.00090.2260.09270.050.0816-0.01140.11010.0151-0.07080.0556-0.00460.248332.479-15.008-35.908
82.6008-2.1967-1.9324.5334-1.15044.4207-0.1318-0.0055-0.1890.16520.23920.28950.152-0.2237-0.10740.19120.0063-0.0250.0695-0.03320.305630.359-13.63-33.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 12
2X-RAY DIFFRACTION2E1 - 12
3X-RAY DIFFRACTION3A1 - 12
4X-RAY DIFFRACTION4B1 - 12
5X-RAY DIFFRACTION5C1 - 12
6X-RAY DIFFRACTION6F1 - 12
7X-RAY DIFFRACTION7G1 - 12
8X-RAY DIFFRACTION8H1 - 12

+
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