[English] 日本語
Yorodumi
- PDB-9he5: Crystal structure of the oxidized respiratory complex I subunit N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9he5
TitleCrystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V90P(NuoE)
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / NADH oxidoreductase / respiratory chain / iron-sulfur-cluster / flavin
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / quinone binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain ...Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsWohlwend, D. / Gerhardt, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1140/11-2 (SPP 1927) Germany
CitationJournal: To Be Published
Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I
Authors: Wohlwend, D. / Gnandt, E. / Vranas, M. / Gerhardt, S. / Friedrich, T.
History
DepositionNov 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,39614
Polymers134,1904
Non-polymers2,20610
Water10,665592
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2218
Polymers67,0952
Non-polymers1,1266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-97 kcal/mol
Surface area21770 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1756
Polymers67,0952
Non-polymers1,0804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-81 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.246, 64.326, 121.576
Angle α, β, γ (deg.)90.000, 106.347, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

#1: Protein NADH-quinone oxidoreductase subunit E / NADH dehydrogenase I subunit E / NDH-1 subunit E


Mass: 18571.602 Da / Num. of mol.: 2 / Mutation: V90P
Source method: isolated from a genetically manipulated source
Details: Mutation V90P was introduced by site-directed mutagenesis
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-Blue1::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit F


Mass: 48523.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence AGHHHHHH is a C-terminal affinity tag not found in the wild-type protein
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-Blue1::nuoEFhis / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: O66841

-
Non-polymers , 6 types, 602 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 6.8-7.1, 0.8-1.05 M Na3Citrat, 0.1 M NaCl
PH range: 6.8-7.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2012 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→116.661 Å / Num. obs: 122759 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.042 / Rrim(I) all: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 1.84→2.06 Å / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.461 / Num. measured all: 129219 / Num. unique obs: 34743 / CC1/2: 0.857 / Rpim(I) all: 0.275 / Rrim(I) all: 0.539 / Net I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.1.29data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.844→116.661 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.69 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 6164 5.022 %Random selection
Rwork0.1678 116572 --
all0.169 ---
obs-122736 99.634 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.714 Å20 Å2-1.322 Å2
2--0.391 Å2-0 Å2
3---0.938 Å2
Refinement stepCycle: LAST / Resolution: 1.844→116.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 98 592 9772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168907
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.85212818
X-RAY DIFFRACTIONr_angle_other_deg0.4561.76420636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.918550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.037101613
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.36710421
X-RAY DIFFRACTIONr_chiral_restr0.0690.21351
X-RAY DIFFRACTIONr_chiral_restr_other0.0240.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022059
X-RAY DIFFRACTIONr_nbd_refined0.2080.21811
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.28026
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24573
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2541
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0560.22
X-RAY DIFFRACTIONr_nbd_other0.1310.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.222
X-RAY DIFFRACTIONr_mcbond_it1.4842.6744578
X-RAY DIFFRACTIONr_mcbond_other1.4842.6744578
X-RAY DIFFRACTIONr_mcangle_it2.2854.8015717
X-RAY DIFFRACTIONr_mcangle_other2.2854.8025718
X-RAY DIFFRACTIONr_scbond_it2.1623.0094866
X-RAY DIFFRACTIONr_scbond_other2.1633.0054843
X-RAY DIFFRACTIONr_scangle_it3.5695.4087070
X-RAY DIFFRACTIONr_scangle_other3.575.3967047
X-RAY DIFFRACTIONr_lrange_it4.8425.94610563
X-RAY DIFFRACTIONr_lrange_other4.77125.5410449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.844-1.8920.3044510.28785540.28890520.9370.94399.48080.266
1.892-1.9440.2834380.2583560.25188070.950.95899.85240.227
1.944-20.2354330.22281560.22385910.9630.96699.97670.2
2-2.0620.2284100.20579220.20683370.9620.97199.940.184
2.062-2.1290.2353940.19476820.19680940.9630.97599.77760.174
2.129-2.2040.2094200.18473750.18578050.9720.97899.87190.162
2.204-2.2870.2163590.17772020.17975870.9710.9899.65730.156
2.287-2.3810.23970.16768370.16972430.9770.98399.87570.146
2.381-2.4860.1673390.15766640.15870070.9810.98599.94290.141
2.486-2.6080.1753330.15763190.15866590.9810.98599.89490.14
2.608-2.7490.1982970.15960850.16163940.9770.98499.81230.145
2.749-2.9150.1793120.15457040.15560330.980.98599.71820.143
2.915-3.1160.1922890.16953570.1756620.9770.98299.71740.16
3.116-3.3660.192550.16850220.16952860.9770.98499.82970.167
3.366-3.6870.172460.16745780.16748680.9860.98599.09610.17
3.687-4.1220.1461980.14141660.14144190.9880.98998.75540.15
4.122-4.7580.1561950.12536620.12639010.9880.99198.87210.141
4.758-5.8250.1751760.1531300.15133400.9860.9998.9820.166
5.825-8.2280.1551470.1524140.1525900.9860.98998.88030.169
8.228-116.6610.223750.16613870.16914870.9770.97898.31880.203

+
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