[English] 日本語
Yorodumi
- PDB-8evm: De novo design of chlorophyll special pair containing protein ass... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8evm
TitleDe novo design of chlorophyll special pair containing protein assemblies
ComponentsChlorophyll dimer protein designs, Special Pair 3 (SP3x)
KeywordsDE NOVO PROTEIN / de novo design / chlorophyll / electron donor / photosynthetic
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBera, A.K. / Ennist, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Chem Biol / Year: 2024
Title: De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh ...Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh Hua / Arundhati P Deshmukh / Adam P Moyer / Derrick R Hicks / Avi Z Swartz / Ralph A Cacho / Nathan Novy / Asim K Bera / Alex Kang / Banumathi Sankaran / Matthew P Johnson / Amala Phadkule / Mike Reppert / Damian Ekiert / Gira Bhabha / Lance Stewart / Justin R Caram / Barry L Stoddard / Elisabet Romero / C Neil Hunter / David Baker /
Abstract: Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer ...Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chlorophyll dimer protein designs, Special Pair 3 (SP3x)
C: Chlorophyll dimer protein designs, Special Pair 3 (SP3x)


Theoretical massNumber of molelcules
Total (without water)51,6422
Polymers51,6422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-30 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.732, 88.732, 149.484
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Chlorophyll dimer protein designs, Special Pair 3 (SP3x)


Mass: 25820.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Sodium malonate dibasic monohydrate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.05→44.37 Å / Num. obs: 13483 / % possible obs: 99.42 % / Redundancy: 10.8 % / Biso Wilson estimate: 112.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.194 / Net I/σ(I): 11.54
Reflection shellResolution: 3.05→3.15 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 1311 / CC1/2: 0.248 / % possible all: 96.27

-
Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed Protein

Resolution: 3.05→44.37 Å / SU ML: 0.5483 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.1496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2973 1355 10.1 %
Rwork0.2482 12057 -
obs0.253 13412 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.4 Å2
Refinement stepCycle: LAST / Resolution: 3.05→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 0 0 3539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243557
X-RAY DIFFRACTIONf_angle_d0.51684798
X-RAY DIFFRACTIONf_chiral_restr0.0301596
X-RAY DIFFRACTIONf_plane_restr0.0018613
X-RAY DIFFRACTIONf_dihedral_angle_d14.57091344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.160.40141300.37841134X-RAY DIFFRACTION96.27
3.16-3.290.38241400.34021176X-RAY DIFFRACTION99.32
3.29-3.430.35451320.33821186X-RAY DIFFRACTION99.77
3.44-3.620.37891390.31641184X-RAY DIFFRACTION99.92
3.62-3.840.35511360.30411204X-RAY DIFFRACTION99.93
3.84-4.140.37291390.26321189X-RAY DIFFRACTION99.85
4.14-4.550.30961370.26171216X-RAY DIFFRACTION100
4.56-5.210.31341370.2721213X-RAY DIFFRACTION100
5.21-6.560.35631360.3171232X-RAY DIFFRACTION99.93
6.57-44.370.19261290.16821323X-RAY DIFFRACTION99.52

+
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