[English] 日本語
Yorodumi
- PDB-8qh4: Crystal structure of reduced respiratory Complex I subunits NuoEF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qh4
TitleCrystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Complex I / Respiratory Chain / 3-acetylpyridine dinucleotide / NADH-binding
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
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-FNR / : / 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 / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsWohlwend, D. / Friedrich, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I.
Authors: Wohlwend, D. / Merono, L. / Bucka, S. / Ritter, K. / Jessen, H.J. / Friedrich, T.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
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)138,57030
Polymers134,1944
Non-polymers4,37626
Water15,709872
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,24015
Polymers67,0972
Non-polymers2,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-188 kcal/mol
Surface area21270 Å2
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,33015
Polymers67,0972
Non-polymers2,23313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-140 kcal/mol
Surface area20900 Å2
Unit cell
Length a, b, c (Å)63.527, 116.619, 190.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 18573.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pET-28b(+) / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3)
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 / Mutation: 427AGHHHHHH
Source method: isolated from a genetically manipulated source
Details: Sequence AGHHHHHH was added to the C-terminus via molecular biology techniques to allow for affinity purification
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF / Plasmid: pET-28b(+) / Production host: Escherichia coli B (bacteria) / Strain (production host): Rosetta 2(DE3) / References: UniProt: O66841

-
Non-polymers , 9 types, 898 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-A3D / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE


Mass: 662.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: trisodium citrate, ammonium sulfate, sodium chloride, Tris, BisTris
PH range: 6.3 - 7.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→48.153 Å / Num. obs: 102156 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 14.4
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4996 / CC1/2: 0.864 / Rpim(I) all: 0.318 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimless0.7.9data scaling
REFMAC5.8.0352phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.96→48.153 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.161 / SU B: 7.85 / SU ML: 0.112 / Average fsc free: 0.9569 / Average fsc work: 0.9667 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2244 5246 5.181 %
Rwork0.1919 96010 -
all0.194 --
obs-101256 99.166 %
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: 25.256 Å2
Baniso -1Baniso -2Baniso -3
1--0.583 Å2-0 Å2-0 Å2
2--1.355 Å20 Å2
3----0.772 Å2
Refinement stepCycle: LAST / Resolution: 1.96→48.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 214 872 10170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168731
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.65112981
X-RAY DIFFRACTIONr_angle_other_deg0.41.57120399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20851150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.223553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62101618
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.351011
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.79510423
X-RAY DIFFRACTIONr_chiral_restr0.0590.21379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
X-RAY DIFFRACTIONr_nbd_refined0.2150.21991
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.28230
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24634
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2753
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.214
X-RAY DIFFRACTIONr_nbd_other0.1460.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1370.21
X-RAY DIFFRACTIONr_mcbond_it0.6661.3614600
X-RAY DIFFRACTIONr_mcbond_other0.6651.3624600
X-RAY DIFFRACTIONr_mcangle_it1.1082.0365750
X-RAY DIFFRACTIONr_mcangle_other1.1082.0375751
X-RAY DIFFRACTIONr_scbond_it0.9721.5434971
X-RAY DIFFRACTIONr_scbond_other0.8911.5164944
X-RAY DIFFRACTIONr_scangle_it1.5732.2717203
X-RAY DIFFRACTIONr_scangle_other1.4772.2287162
X-RAY DIFFRACTIONr_lrange_it5.71120.88211060
X-RAY DIFFRACTIONr_lrange_other5.54719.1610847
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
1.96-2.0110.2613960.24770680.24874640.9520.9571000.209
2.011-2.0660.2623720.23268840.23472570.9510.96399.98620.193
2.066-2.1260.2523810.21666900.21870710.9590.9681000.178
2.126-2.1910.2493590.20565220.20768840.960.97399.95640.168
2.191-2.2630.4553220.41657820.41866520.7940.81591.76190.382
2.263-2.3420.2423370.22158550.22264420.9680.97396.11920.175
2.342-2.430.2263220.17859310.18162530.970.9811000.146
2.43-2.5290.2223030.17656860.17859890.9710.9811000.145
2.529-2.6410.2053140.18154850.18257990.9720.9811000.148
2.641-2.770.2152840.18152330.18355170.9720.981000.151
2.77-2.9190.2272730.17149840.17452580.9720.98299.9810.145
2.919-3.0950.2092510.17847380.17949890.9730.9811000.155
3.095-3.3080.2232680.18744350.18947030.9690.9791000.167
3.308-3.5720.232240.18241730.18543980.9680.98199.97730.164
3.572-3.910.2051870.18338620.18440680.9760.9899.53290.162
3.91-4.3680.1641700.14334950.14436820.9850.98999.53830.133
4.368-5.0370.1751660.14531200.14632860.9840.9891000.136
5.037-6.1520.2031530.16426650.16628180.9780.9871000.151
6.152-8.6310.1661090.15721150.15722240.9860.9871000.148
8.631-48.1530.18550.19312880.19213440.9820.9899.92560.181
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2848-0.76270.49230.9419-0.04041.63480.19420.1987-0.4724-0.0957-0.01130.15870.5629-0.0142-0.18290.3182-0.016-0.07220.0444-0.02960.105127.2857-10.6863-60.2711
21.37290.0429-0.19330.3684-0.16621.76660.02770.03520.08590.00020.0519-0.0091-0.1038-0.0249-0.07960.0954-0.0099-0.00440.00950.0020.010425.772312.5877-54.5443
32.84520.6289-0.37480.8861-0.03061.44950.1776-0.3060.59810.0773-0.06530.1576-0.45990.0492-0.11240.262-0.00590.0520.0617-0.05560.1303-4.146511.0901-12.5482
41.6655-0.03050.4650.3535-0.08641.53260.10260.024-0.1398-0.007-0.0175-0.00630.12790.0927-0.08510.10730.0276-0.00610.0181-0.00170.0143-5.6849-11.9744-18.6271
Refinement TLS groupSelection: ALL

+
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