[English] 日本語
Yorodumi
- PDB-1sip: ALTERNATIVE NATIVE FLAP CONFORMATION REVEALED BY 2.3 ANGSTROMS RE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sip
TitleALTERNATIVE NATIVE FLAP CONFORMATION REVEALED BY 2.3 ANGSTROMS RESOLUTION STRUCTURE OF SIV PROTEINASE
ComponentsUNLIGANDED SIV PROTEASE
KeywordsHYDROLASE(ACID PROTEINASE)
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWilderspin, A.F.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.
Authors: Wilderspin, A.F. / Sugrue, R.J.
#1: Journal: Protein Expr.Purif. / Year: 1994
Title: Purification of Crystallizable Recombinant Sivmac251-32H Proteinase
Authors: Sugrue, R.J. / Almond, N. / Kitchin, P. / Richardson, S.M.H. / Wilderspin, A.F.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Investigation of Recombinant Simian Immunodeficiency Virus Proteinase
Authors: Wilderspin, A.F. / Sugrue, R.J.
History
DepositionApr 13, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE STRANDS IN THE *SHEET* RECORDS CORRESPOND TO THE NOTATION IN *JRNL* AS FOLLOWS. 1=B, 2=C, ...SHEET THE STRANDS IN THE *SHEET* RECORDS CORRESPOND TO THE NOTATION IN *JRNL* AS FOLLOWS. 1=B, 2=C, 3=D', 4=D, 5=C', 6=B', 7=A'. THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINAL STRANDS FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTI-PARALLEL BETA-SHEET, S2. APPLICATION OF THE TWO-FOLD ROTATION TO RESIDUES 2 - 4 AND 95 - 99 GENERATES RESIDUES 2' - 4' AND 95' - 99', RESPECTIVELY. BECAUSE OF THE LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT, IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON *SHEET* RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. STRANDS 1 AND 3 ARE FROM THE MOLECULE IN THIS ENTRY, AND ARE TERMED STRAND A AND STRAND T IN *JRNL*; STRANDS 2 AND 4 ARE FROM THE SYMMETRY-RELATED MOLECULE. S2 4 GLN 2 SER 4 0 S2 4 MET 95' PHE 99' -1 S2 4 MET 95 PHE 99 -1 S2 4 GLN 2' SER 4' -1

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UNLIGANDED SIV PROTEASE


Theoretical massNumber of molelcules
Total (without water)10,7871
Polymers10,7871
Non-polymers00
Water72140
1
A: UNLIGANDED SIV PROTEASE

A: UNLIGANDED SIV PROTEASE


Theoretical massNumber of molelcules
Total (without water)21,5752
Polymers21,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3560 Å2
ΔGint-25 kcal/mol
Surface area9820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)32.180, 62.520, 95.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-100-

HOH

21A-101-

HOH

-
Components

#1: Protein UNLIGANDED SIV PROTEASE


Mass: 10787.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Cell line: S2 / Organ: LEAVES
References: UniProt: Q87706, UniProt: Q88016*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE THREE SEQUENCE VARIATIONS BETWEEN SIVMAC251-32H SHOWN IN SEQRES AND THE DATA BASE ENTRY ...THERE ARE THREE SEQUENCE VARIATIONS BETWEEN SIVMAC251-32H SHOWN IN SEQRES AND THE DATA BASE ENTRY FOR SIVMAC251, NAMELY E63K, R72K AND F99L. THERE IS ONE VARIATION WITH ENTRY SIVMAC239, NAMELY R72K. THESE VARIATIONS ARE DESCRIBED IN REFERENCE 1.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlproteinase1drop
2100 mMsodium acetate1reservoir
30.2 M1reservoirNaCl

-
Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 4457 / % possible obs: 97.7 % / Num. measured all: 25196 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.46 Å / % possible obs: 89.8 %

-
Processing

Software
NameClassification
RESTRAINrefinement
FRODOmodel building
RefinementResolution: 2.3→8 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.17 4457 97.7 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 0 40 800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
Refinement
*PLUS
Num. reflection all: 4457 / Rfactor all: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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