[English] 日本語
Yorodumi
- PDB-4y6k: Complex structure of presenilin homologue PSH bound to an inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y6k
TitleComplex structure of presenilin homologue PSH bound to an inhibitor
ComponentsUncharacterized protein PSH
KeywordsMEMBRANE PROTEIN/INHIBITOR / Complex / Inhibitor / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


aspartic endopeptidase activity, intramembrane cleaving / membrane / identical protein binding
Similarity search - Function
Signal-peptide peptidase, presenilin aspartyl protease / Signal-peptide peptidase, presenilin aspartyl protease / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family
Similarity search - Domain/homology
N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide / Chem-4B5 / Signal peptide peptidase
Similarity search - Component
Biological speciesMethanoculleus marisnigri JR1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.855 Å
AuthorsDang, S. / Wu, S. / Wang, J. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH
Authors: Dang, S. / Wu, S. / Wang, J. / Li, H. / Huang, M. / He, W. / Li, Y.M. / Wong, C.C. / Shi, Y.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Non-polymer description
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein PSH
B: Uncharacterized protein PSH
C: Uncharacterized protein PSH
D: Uncharacterized protein PSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8636
Polymers127,5174
Non-polymers1,3462
Water0
1
A: Uncharacterized protein PSH
B: Uncharacterized protein PSH

A: Uncharacterized protein PSH
B: Uncharacterized protein PSH


Theoretical massNumber of molelcules
Total (without water)127,5174
Polymers127,5174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7570 Å2
ΔGint-78 kcal/mol
Surface area50780 Å2
MethodPISA
2
C: Uncharacterized protein PSH
D: Uncharacterized protein PSH
hetero molecules

C: Uncharacterized protein PSH
D: Uncharacterized protein PSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2088
Polymers127,5174
Non-polymers2,6914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area8430 Å2
ΔGint-79 kcal/mol
Surface area50010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.617, 201.691, 117.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein
Uncharacterized protein PSH


Mass: 31879.260 Da / Num. of mol.: 4 / Mutation: D40N, E42S, A147E, V148P, A229V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanoculleus marisnigri JR1 (archaea)
Strain: JR1 / Gene: Memar_1924 / Production host: Escherichia coli (E. coli) / References: UniProt: A3CWV0
#2: Chemical ChemComp-4B5 / N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 672.853 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H52N4O6
References: N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Glycine pH 3.6, 0.2 M (NH4)2SO4, 20% (w/v) PEG500MME, 6% (w/v) Glycerol, 0.04% (w/v) Anapoe-C12E8,1% (w/v) N-heptyl-b-D-thioglucoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RIGAKU SATURN 724 / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 7729 / % possible obs: 51 % / Redundancy: 6.5 % / Net I/σ(I): 8.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYG

4hyg


Resolution: 3.855→48.203 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 47.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3675 361 4.67 %
Rwork0.3199 --
obs0.3222 7725 40.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.855→48.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 98 0 7200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067351
X-RAY DIFFRACTIONf_angle_d1.49510038
X-RAY DIFFRACTIONf_dihedral_angle_d19.2682475
X-RAY DIFFRACTIONf_chiral_restr0.0581295
X-RAY DIFFRACTIONf_plane_restr0.0111187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8545-4.4120.3465540.28921017X-RAY DIFFRACTION17
4.412-5.55730.3596880.29651889X-RAY DIFFRACTION31
5.5573-48.20630.37952190.34284458X-RAY DIFFRACTION71
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)
11.0899-0.23430.03171.1930.05771.2434-0.27040.05980.0606-0.2875-0.25390.0794-0.0124-0.2537-0.11010.3339-0.03620.19820.60260.05650.575104.605792.104931.5358
20.5154-0.0284-0.23380.9480.44191.3017-0.0644-0.098-0.1510.1111-0.2265-0.01930.2362-0.2754-0.00340.44360.08530.1610.72240.21250.621105.317674.515867.7764
30.63360.00590.1420.61630.0490.8284-0.28470.03810.4157-0.012-0.1403-0.055-0.43360.089-0.29880.57430.2303-0.86710.8709-0.01850.5099148.1464126.0922104.3259
40.35980.152-0.12830.5958-0.17391.057-0.26370.12360.18160.1401-0.20570.2657-0.4573-0.0245-0.03420.35990.0267-0.02230.8464-0.35470.7896148.4218112.8205143.0595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:293
2X-RAY DIFFRACTION2chain B and resid 7:291
3X-RAY DIFFRACTION3chain C and resid 4:293
4X-RAY DIFFRACTION4chain D and resid 6:291

+
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