[English] 日本語
Yorodumi
- PDB-6q9c: Crystal structure of Aquifex aeolicus NADH-quinone oxidoreductase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q9c
TitleCrystal structure of Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF bound to NADH under anaerobic conditions
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / respiratory chain / complex I / NADH ubiquinone oxidoreductase / Fe-S clusters
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 / NADH-ubiquinone oxidoreductase 51kDa subunit / Ubiquitin-like (UB roll) - #600 / 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. ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / Ubiquitin-like (UB roll) - #600 / 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 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsWohlwend, D. / Gerhardt, S. / Gnandt, E. / Friedrich, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 1976 Germany
CitationJournal: Nat Commun / Year: 2019
Title: A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.
Authors: Schulte, M. / Frick, K. / Gnandt, E. / Jurkovic, S. / Burschel, S. / Labatzke, R. / Aierstock, K. / Fiegen, D. / Wohlwend, D. / Gerhardt, S. / Einsle, O. / Friedrich, T.
History
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
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)133,70027
Polymers129,3464
Non-polymers4,35423
Water17,312961
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,83713
Polymers64,6732
Non-polymers2,16411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-122 kcal/mol
Surface area21380 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86414
Polymers64,6732
Non-polymers2,19112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-145 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.279, 115.829, 189.832
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: 17935.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoE, aq_574 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66842, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 46737.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoF, aq_573 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66841, NADH dehydrogenase (quinone)

-
Non-polymers , 8 types, 984 molecules

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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.69 Å3/Da / Density % sol: 54.26 % / Mosaicity: 0.1 °
Crystal growTemperature: 281 K / Method: evaporation / pH: 6.5
Details: (NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: Fixed-exit LN2 cooled Double Si (111) Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→49.44 Å / Num. obs: 134290 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.055 / Rrim(I) all: 0.205 / Net I/σ(I): 7.2 / Num. measured all: 1835069 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.8113.81.49866110.8130.4151.555100
9.75-49.4412.20.1059550.9960.0320.1199.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→49.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.936 / SU ML: 0.087 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 6946 5.2 %RANDOM
Rwork0.1795 ---
obs0.1809 127230 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 29.32 Å2 / Biso min: 17.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--1.12 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.78→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 234 961 10299
Biso mean--29.24 40.59 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178921
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.65313063
X-RAY DIFFRACTIONr_angle_other_deg1.2021.58820763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17951154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91322.651479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.353151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4861553
X-RAY DIFFRACTIONr_chiral_restr0.0590.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021961
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 515 -
Rwork0.266 9302 -
all-9817 -
obs--99.96 %
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)
13.4149-5.5237-1.508111.48114.06632.4544-0.00340.012-0.58270.4337-0.13510.4280.62420.05760.13850.322-0.0926-0.02130.25770.07230.416110.3645-18.0007-58.0434
24.0889-1.8972-1.38143.66251.31362.7580.12770.2354-0.5376-0.0947-0.10990.3410.3092-0.1523-0.01770.1977-0.0834-0.06630.15530.01310.182213.9403-11.3169-62.4751
33.5965-0.95850.80533.3907-0.43582.45120.16380.3198-0.4458-0.2341-0.01360.35370.3489-0.1887-0.15020.2275-0.0548-0.06980.1894-0.03810.115614.3916-8.4908-68.4867
42.38260.22220.87813.5577-0.3341.79520.07940.2777-0.36-0.30960.05720.02350.31330.0223-0.13660.18160.0185-0.01970.2031-0.02710.056934.3978-8.0749-61.1809
53.17080.66970.31425.51561.26832.0782-0.06570.2126-0.375-0.30810.162-0.41110.35380.3656-0.09620.24860.0687-0.01410.2298-0.02420.0842.5078-12.9902-60.629
61.3291-0.14690.19753.2203-0.62341.83540.0924-0.0477-0.22210.05630.0166-0.10530.25830.1713-0.1090.13620.0227-0.04070.1846-0.00580.04938.5801-7.8908-52.4498
71.6240.01770.11410.5582-0.0651.2173-0.0156-0.11780.07920.06120.06510.0332-0.0839-0.0686-0.04950.0845-0.01140.00440.1260.01660.010421.924612.6822-48.8912
83.49480.00720.50741.02490.24272.64690.00390.11150.051-0.03720.0208-0.2009-0.0460.3279-0.02470.109-0.02810.01280.15470.00190.040739.747912.3297-73.6868
95.35462.56977.7994.17364.68811.674-0.2112-0.09810.3539-0.0674-0.30370.4097-0.2774-0.22780.51490.35940.03890.02040.2372-0.02210.5384-20.318621.8825-14.1285
104.79571.96542.81353.16861.77773.17270.0143-0.00510.7622-0.0382-0.02590.4306-0.3069-0.14660.01160.18550.0920.07630.12850.01910.2954-20.42469.371-13.5477
112.17180.3158-0.63610.8585-0.16010.93350.1984-0.30930.67640.1555-0.05070.2409-0.36830.0109-0.14770.26920.00730.07050.1939-0.0980.2423-9.983311.7637-6.6259
122.75820.2639-0.19726.8190.66861.34620.0107-0.35210.37560.34060.1725-0.4517-0.22920.3604-0.18320.2066-0.06790.01150.2523-0.02280.134112.460910.9012-11.7038
132.55210.3408-0.20392.4193-0.09730.53320.14130.0510.39310.1901-0.08140.1273-0.20020.1781-0.05990.1506-0.02820.04130.15820.00990.06643.95837.304-16.6473
146.0763-3.0413-0.88625.87670.79223.03010.12130.21370.567-0.1248-0.0830.0931-0.39750.2716-0.03820.1914-0.07380.05290.22710.02850.131211.023213.2474-23.2601
152.08370.16690.16320.70810.0251.73810.07620.2024-0.0538-0.0405-0.00210.06380.084-0.0803-0.07410.08120.0405-0.01430.11240.00030.0117-15.5457-9.0387-24.4051
161.0695-0.2724-0.29490.26090.21993.17560.0830.0416-0.18410.0106-0.0659-0.06980.22720.3233-0.01710.12420.0469-0.01420.15560.01710.10957.2935-15.3648-10.9091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 21
2X-RAY DIFFRACTION2A22 - 51
3X-RAY DIFFRACTION3A52 - 74
4X-RAY DIFFRACTION4A75 - 93
5X-RAY DIFFRACTION5A94 - 121
6X-RAY DIFFRACTION6A122 - 160
7X-RAY DIFFRACTION7B3 - 326
8X-RAY DIFFRACTION8B327 - 419
9X-RAY DIFFRACTION9C8 - 14
10X-RAY DIFFRACTION10C15 - 39
11X-RAY DIFFRACTION11C40 - 90
12X-RAY DIFFRACTION12C91 - 118
13X-RAY DIFFRACTION13C119 - 144
14X-RAY DIFFRACTION14C145 - 160
15X-RAY DIFFRACTION15D3 - 236
16X-RAY DIFFRACTION16D237 - 418

+
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