[English] 日本語
Yorodumi
- PDB-6c4x: Cross-alpha Amyloid-like Structure alphaAmmem -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c4x
TitleCross-alpha Amyloid-like Structure alphaAmmem
Componentscross-alpha amyloid-like membrane peptide alpha-AmMEM
KeywordsDE NOVO PROTEIN / Protein Design / Cross-alpha Amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.55 Å
AuthorsLiu, L. / Zhang, S.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM122603 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Designed peptides that assemble into cross-alpha amyloid-like structures.
Authors: Zhang, S.Q. / Huang, H. / Yang, J. / Kratochvil, H.T. / Lolicato, M. / Liu, Y. / Shu, X. / Liu, L. / DeGrado, W.F.
History
DepositionJan 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cross-alpha amyloid-like membrane peptide alpha-AmMEM
B: cross-alpha amyloid-like membrane peptide alpha-AmMEM
C: cross-alpha amyloid-like membrane peptide alpha-AmMEM
D: cross-alpha amyloid-like membrane peptide alpha-AmMEM
E: cross-alpha amyloid-like membrane peptide alpha-AmMEM
F: cross-alpha amyloid-like membrane peptide alpha-AmMEM
G: cross-alpha amyloid-like membrane peptide alpha-AmMEM
H: cross-alpha amyloid-like membrane peptide alpha-AmMEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,78110
Polymers22,5978
Non-polymers1842
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Fibrils confirmed by Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-142 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.676, 82.676, 155.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein/peptide
cross-alpha amyloid-like membrane peptide alpha-AmMEM


Mass: 2824.621 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 35% MPD, 0.2 M MgCl2 and imidazole 0.1 M pH 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 3.55→72 Å / Num. obs: 7070 / % possible obs: 97.9 % / Redundancy: 4.1 % / Net I/σ(I): 6.4
Reflection shellResolution: 3.55→3.77 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 3.55→71.6 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.952 / SU B: 58.227 / SU ML: 0.844 / Cross valid method: THROUGHOUT / ESU R Free: 0.727 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34514 206 5 %RANDOM
Rwork0.30746 ---
obs0.30948 3944 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 96.592 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å21.63 Å20 Å2
2--3.26 Å2-0 Å2
3----10.56 Å2
Refinement stepCycle: 1 / Resolution: 3.55→71.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 9 3 1335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191336
X-RAY DIFFRACTIONr_bond_other_d0.0020.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.3682.0291824
X-RAY DIFFRACTIONr_angle_other_deg0.99233056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5545187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23724.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47515204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021419
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02221
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_it6.00610.508772
X-RAY DIFFRACTIONr_mcbond_other6.00110.509771
X-RAY DIFFRACTIONr_mcangle_it9.98315.679951
X-RAY DIFFRACTIONr_mcangle_other9.97815.681952
X-RAY DIFFRACTIONr_scbond_it5.92611.353564
X-RAY DIFFRACTIONr_scbond_other5.92111.357565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.35616.773874
X-RAY DIFFRACTIONr_long_range_B_refined18.0455201
X-RAY DIFFRACTIONr_long_range_B_other18.0435202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.55→3.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 10 -
Rwork0.37 287 -
obs--100 %

+
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