[English] 日本語
Yorodumi
- PDB-6a7k: X-ray structure of NdhS from T. elongatus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a7k
TitleX-ray structure of NdhS from T. elongatus
ComponentsTlr0636 protein
KeywordsELECTRON TRANSPORT / NADH dehydrogenase-like complex / NDH-1 / cyclic electron flow (CEF) / Ferredoxin
Function / homologyNADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / photosynthetic electron transport chain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta / ACETIC ACID / Tlr0636 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUmeno, K. / Misumi, Y. / Tanaka, H. / Kurisu, G.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Japan
CitationJournal: Science / Year: 2019
Title: Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.
Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa ...Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa Ikegami / Benjamin D Engel / Genji Kurisu / Marc M Nowaczyk /
Abstract: Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
History
DepositionJul 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tlr0636 protein
B: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5674
Polymers16,4472
Non-polymers1202
Water1,910106
1
A: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2842
Polymers8,2241
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tlr0636 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2842
Polymers8,2241
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-0 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.850, 58.850, 225.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 4 - 61 / Label seq-ID: 4 - 61

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Tlr0636 protein / NdhS


Mass: 8223.556 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tlr0636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DL61
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Sodium acetate trihydrate (pH 4.6), 100mM CdCl2, 38 % (v/v) polyethylene glycol (PEG) 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→49.71 Å / Num. obs: 19195 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 8.25 / Num. unique obs: 2520 / CC1/2: 0.985 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSVERSION Jan 26, 2018data reduction
XDSVERSION Jan 26, 2018data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4S

3c4s


Resolution: 1.9→49.71 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.858 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23783 960 5 %RANDOM
Rwork0.21858 ---
obs0.21957 18235 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.596 Å2
Baniso -1Baniso -2Baniso -3
1-8.77 Å20 Å20 Å2
2--8.77 Å20 Å2
3----17.55 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 8 106 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02981
X-RAY DIFFRACTIONr_bond_other_d0.0020.02923
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9651335
X-RAY DIFFRACTIONr_angle_other_deg1.07832144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.19226.1942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1915166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.359152
X-RAY DIFFRACTIONr_chiral_restr0.1680.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02181
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_it3.2062.484489
X-RAY DIFFRACTIONr_mcbond_other3.0532.473486
X-RAY DIFFRACTIONr_mcangle_it4.4153.679607
X-RAY DIFFRACTIONr_mcangle_other4.4283.683608
X-RAY DIFFRACTIONr_scbond_it4.932.966492
X-RAY DIFFRACTIONr_scbond_other4.9252.97493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9294.288729
X-RAY DIFFRACTIONr_long_range_B_refined9.98732.2171003
X-RAY DIFFRACTIONr_long_range_B_other9.98432.2591004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2968 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 68 -
Rwork0.19 1289 -
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