[English] 日本語
Yorodumi
- PDB-4mh8: The crystal structure of the monomeric reverse transcriptase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mh8
TitleThe crystal structure of the monomeric reverse transcriptase from moloney murine leukemia virus
ComponentsReverse transcriptase/ribonuclease H p80
KeywordsTRANSFERASE / HYDROLASE / REPLICATION / RNA AND DNA DEPENDENT DNA POLYMERASE / REVERSE TRANSCRIPTASE
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #370 / RNase H-like domain found in reverse transcriptase / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 ...Ubiquitin-like (UB roll) - #370 / RNase H-like domain found in reverse transcriptase / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ubiquitin-like (UB roll) / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDas, D. / Georgiadis, M.M.
CitationJournal: Structure / Year: 2004
Title: The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.
Authors: Das, D. / Georgiadis, M.M.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 16, 2013ID: 1RW3
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H p80


Theoretical massNumber of molelcules
Total (without water)72,5741
Polymers72,5741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)242.332, 94.621, 52.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Reverse transcriptase/ribonuclease H p80 / RT


Mass: 72573.547 Da / Num. of mol.: 1 / Mutation: L435K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Strain: isolate Shinnick / Gene: gag-pol / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03355, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-671) WAS EXPRESSED WITH A PURIFICATION TAG. THE TAG WAS REMOVED LEAVING ...THIS CONSTRUCT (RESIDUES 24-671) WAS EXPRESSED WITH A PURIFICATION TAG. THE TAG WAS REMOVED LEAVING RESIDUES GSHM FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, PEG 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 300

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11081
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X2510.9196
SYNCHROTRONAPS 19-ID20.9794
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJun 28, 2001
CUSTOM-MADE2CCDOct 18, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91961
20.97941
ReflectionResolution: 3→40 Å / Num. obs: 22526 / Observed criterion σ(I): -3 / Redundancy: 3.8 %
Reflection shellResolution: 3→3.11 Å / % possible all: 89.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
CNSrefinement
MLPHAREphasing
PHASERphasing
PHENIXmodel building
AMoREphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
PHENIXphasing
RefinementMethod to determine structure: MIRAS, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAJ, 4HKQ

1qaj

4hkq


Resolution: 3→39.636 Å / SU ML: 0.38 / σ(F): 1 / Phase error: 30.2 / Stereochemistry target values: ML
Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.THE STRUCTURE WAS ORIGINALLY SOLVED IN 2004 USING A COMBINATION OF MIRAS ...Details: 1.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2.THE STRUCTURE WAS ORIGINALLY SOLVED IN 2004 USING A COMBINATION OF MIRAS AND MOLECULAR REPLACEMENT USING 1QAJ.PDB AND DEPOSITED IN THE PDB AS 1RW3.PDB. THE STRUCTURE WAS RE-REFINED IN 2013 USING THE SAME X-RAY DATA AND 4HKQ.PDB AS MODEL FOR MOLECULAR REPLACEMENT. SEE REMARK 200 FOR ADDITIONAL DETAILS. 3. RESIDUES 488-671 (UNIPROT ACCESSION P03355, RESIDUES 1147-1330) ARE PRESENT IN THE CRYSTALLIZED PROTEIN. HOWEVER, THEY ARE DISORDERED IN THE STRUCTURE AND MISSING FROM THE MODEL.
RfactorNum. reflection% reflection
Rfree0.2769 1022 4.81 %
Rwork0.2352 --
obs0.2372 21254 84.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 0 0 3580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043679
X-RAY DIFFRACTIONf_angle_d0.7835019
X-RAY DIFFRACTIONf_dihedral_angle_d13.0891384
X-RAY DIFFRACTIONf_chiral_restr0.03562
X-RAY DIFFRACTIONf_plane_restr0.004644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.15830.3216920.27621815X-RAY DIFFRACTION54
3.1583-3.35610.32721100.23532294X-RAY DIFFRACTION69
3.3561-3.6150.27091300.23332782X-RAY DIFFRACTION82
3.615-3.97850.25671730.21213149X-RAY DIFFRACTION94
3.9785-4.55350.23211580.19373269X-RAY DIFFRACTION96
4.5535-5.73420.24951880.21413347X-RAY DIFFRACTION98
5.7342-39.63910.32071710.27933576X-RAY DIFFRACTION99
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)
10.184-0.0523-0.090.20820.02940.0507-0.05620.00840.00660.0465-0.0310.0221-0.12670.0406-0.00020.2519-0.0398-0.03230.13230.01520.1772-57.8180.8181-2.1166
20.018-0.00720.01080.03010.00980.0153-0.08870.2156-0.0323-0.0668-0.14930.16820.0125-0.0502-0.00360.464-0.1389-0.00360.4651-0.01590.2232-76.260624.5272-9.4712
30.0562-0.01440.0310.0427-0.00460.043-0.1064-0.0340.00440.05390.05360.08410.095-0.2006-0.06420.1725-0.21510.14480.4684-0.04220.3255-91.614122.18819.2714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 280)
2X-RAY DIFFRACTION2chain 'A' and (resid 281 through 360)
3X-RAY DIFFRACTION3chain 'A' and (resid 361 through 487)

+
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