[English] 日本語
Yorodumi
- PDB-3zki: BACE2 MUTANT STRUCTURE WITH LIGAND -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zki
TitleBACE2 MUTANT STRUCTURE WITH LIGAND
ComponentsBETA-SECRETASE 2
KeywordsHYDROLASE
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / endoplasmic reticulum / Golgi apparatus / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-WZV / Beta-secretase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBanner, D.W. / Kuglstatter, A. / Benz, J. / Stihle, M. / Ruf, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / ...Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / Kuglstatter, A. / Kusznir, E. / Laeremans, T. / Matile, H. / Miscenic, C. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
History
DepositionJan 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_sheet / struct_site
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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-SECRETASE 2
B: BETA-SECRETASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9664
Polymers84,0952
Non-polymers8712
Water4,468248
1
A: BETA-SECRETASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4832
Polymers42,0471
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-SECRETASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4832
Polymers42,0471
Non-polymers4351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.310, 89.249, 98.850
Angle α, β, γ (deg.)90.00, 96.96, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BETA-SECRETASE 2 / ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR ...ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2 / BETA-SITE APP CLEAVING ENZYME 2 / DOWN REGION ASPARTIC PROTEASE / DRAP / MEMAPSIN-1 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1 / THETA-SECRETASE / BACE2


Mass: 42047.355 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1
#2: Chemical ChemComp-WZV / 5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide


Mass: 435.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20F3N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. ...THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. THE MUTATION HERE IS E269A IN THE PDB FILE AND E331A IN THE DATA BANK SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS PH8.0, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.1 Å / Num. obs: 31592 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.54 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKG

3zkg


Resolution: 2.4→49.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.838 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. MOLECULES A AND B ARE RELATED BY A LOCAL PSEUDO-DYAD AXIS. NCS CONSTRAINTS WERE NOT USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24059 1542 5 %RANDOM
Rwork0.18266 ---
obs0.18561 29125 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.468 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20.22 Å2
2--2.22 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 62 248 5941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9667983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224.217249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5771524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214478
X-RAY DIFFRACTIONr_gen_planes_other
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
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 113 -
Rwork0.298 2073 -
obs--91.96 %

+
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