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Sodium pumping NADH-quinone oxidoreductase with substrate Q2

Electron Microscopy
2.73Å resolution
PDB entry 8a1v coloured by chain, front view.
PDB entry 8a1v coloured by chain, side view.
PDB entry 8a1v coloured by chain, top view.
Source organism: Vibrio cholerae
Assembly composition:
hetero hexamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Na(+)-translocating NADH-quinone reductase
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Multimeric state: hetero hexamer
Accessible surface area: 73167.84 Å2
Buried surface area: 29558.5 Å2
Dissociation area: 1,936.65 Å2
Dissociation energy (ΔGdiss): 23.28 kcal/mol
Dissociation entropy (TΔSdiss): 15.48 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107567

Macromolecules

Na(+)-translocating NADH-quinone reductase subunit A
Chain: A
Length: 468 amino acids
Theoretical weight: 51.13 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5X1 (Residues: 1-446; Coverage: 100%)
Gene names: VC0395_A1884, VC395_2411, nqrA
Pfam:
Na(+)-translocating NADH-quinone reductase subunit A in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit A in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit A in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5X1  
146850100150200250300350400450
 
200400MGSSHHHHHHSSGLEVLFQGPHMITIKKGLDLPIAGTPSQVISDGKAIKKVALLGEEYVGMRPTMHVRVGDEVKKAQILFEDKKNPGVKFTSPVSGKVVEINRGAKRVLQSVVIEVAGDDQVTFDKFEANQLASLNRDAIKTQLVESGLWTAFRTRPFSKVPAIDSTSEAIFVTAMDTNPLAAEPTVVINEQSEAFVAGLDVLSALTTGKVYVCKKGTSLPRSQQPNVEEHVFDGPHPAGLAGTHMHFLYPVSADHVAWSINYQDVIAVGQLFLTGELYTQRVVSLAGPVVNKPRLVRTVMGASLEQLVDSEIMPGEVRIISGSVLSGTKATGPHAYLGRYHLQVSVLREGRDKELFGWAMPGKNKFSVTRSFLGHLFKGQVYNMTTTTNGSDRSMVPIGNYEKVMPLDMEPTLLLRDLCAGDSDSAVRLGALELDEEDLALCTFVCPGKYEYGQLLRECLDKIEKEG
UniProt
A5F5X1
Chains
Secondary structure
Interaction interfaces
Sequence conservation
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Na(+)-translocating NADH-quinone reductase subunit B
Chain: B
Length: 415 amino acids
Theoretical weight: 45.39 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5X0 (Residues: 1-415; Coverage: 100%)
Gene names: VC0395_A1883, VC395_2410, nqrB
Pfam: NQR2, RnfD, RnfE family
Na(+)-translocating NADH-quinone reductase subunit B in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit B in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit B in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5X0  
141550100150200250300350400
 
100200300400MGLKKFLEDIEHHFEPGGKHEKWFALYEAAATLFYTPGLVTKRSSHVRDSVDLKRIMIMVWLAVFPAMFWGMYNAGGQAIAALNHLYSGDQLAAIVAGNWHYWLTEMLGGTMSSDAGWGSKMLLGATYFLPIYATVFIVGGFWEVLFCMVRKHEVNEGFFVTSILFALIVPPTLPLWQAALGITFGVVVAKEVFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAADGYSGATALSQWAQGGAGALINNATGQTITWMDAFIGNIPGSIGEVSTLALMIGAAFIVYMGIASWRIIGGVMIGMILLSTLFNVIGSDTNAMFNMPWHWHLVLGGFAFGMFFMATDPVSASFTNSGKWAYGILIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDHVVVERNIKRRLARYGKQ
UniProt
A5F5X0
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation
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Na(+)-translocating NADH-quinone reductase subunit C
Chain: C
Length: 257 amino acids
Theoretical weight: 27.65 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5Y7 (Residues: 1-257; Coverage: 100%)
Gene names: VC0395_A1882, VC395_2409, nqrC
Pfam: FMN-binding domain
Na(+)-translocating NADH-quinone reductase subunit C in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit C in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit C in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5Y7  
125720406080100120140160180200220240
 
100200MASNNDSIKKTLFVVIALSLVCSIIVSAAAVGLRDKQKENAALDKQSKILQVAGIEAKGSKQIVELFNKSIEPRLVDFNTGDFVEGDAANYDQRKAAKEASESIKLTAEQDKAKIQRRANVGVVYLVKDGDKTSKVILPVHGNGLWSMMYAFVAVETDGNTVSGLTYYEQGETPGLGGEVENPAWRAQWVGKKLFDENHKPAIKIVKGGAPQGSEHGVDGLSGATLTSNGVQNTFDFWLGDMGFGPFLTKVRDGGLN
UniProt
A5F5Y7
Chains
Secondary structure
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Sequence conservation
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Na(+)-translocating NADH-quinone reductase subunit D
Chain: D
Length: 210 amino acids
Theoretical weight: 22.85 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5Y6 (Residues: 1-210; Coverage: 100%)
Gene names: VC0395_A1881, VC395_2408, nqrD
Pfam: Rnf-Nqr subunit, membrane protein
Na(+)-translocating NADH-quinone reductase subunit D in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit D in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit D in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5Y6  
121020406080100120140160180200
 
50100150200MSSAKELKKSVLAPVLDNNPIALQVLGVCSALAVTTKLETAFVMTLAVMFVTALSNFFVSLIRNHIPNSVRIIVQMAIIASLVIVVDQILKAYLYDISKQLSVFVGLIITNCIVMGRAEAFAMKSEPIPSFIDGIGNGLGYGFVLMTVGFFRELLGSGKLFGLEVLPLISNGGWYQPNGLMLLAPSAFFLIGFMIWAIRTFKPEQVEAKE
UniProt
A5F5Y6
Chains
Secondary structure
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Na(+)-translocating NADH-quinone reductase subunit E
Chain: E
Length: 198 amino acids
Theoretical weight: 21.48 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5Y5 (Residues: 1-198; Coverage: 100%)
Gene names: VC0395_A1880, VC395_2407, nqrE
Pfam: Rnf-Nqr subunit, membrane protein
Na(+)-translocating NADH-quinone reductase subunit E in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit E in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit E in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5Y5  
119820406080100120140160180
 
50100150MEHYISLLVKSIFIENMALSFFLGMCTFLAVSKKVKTSFGLGIAVIVVLTISVPVNNLVYNLVLKPDALVEGVDLSFLNFITFIGVIAALVQILEMILDRFFPPLYNALGIFLPLITVNCAIFGGVSFMVQRDYSFAESVVYGFGSGVGWMLAIVALAGIREKMKYSDVPPGLRGLGITFITAGLMALGFMSFSGVQL
UniProt
A5F5Y5
Chains
Secondary structure
Ligand binding sites
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Sequence conservation
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Na(+)-translocating NADH-quinone reductase subunit F
Chain: F
Length: 408 amino acids
Theoretical weight: 45.11 KDa
Source organism: Vibrio cholerae
Expression system: Vibrio cholerae
UniProt:
  • Canonical: A5F5Y4 (Residues: 1-408; Coverage: 100%)
Gene names: VC0395_A1879, VC395_2406, nqrF
Pfam:
Na(+)-translocating NADH-quinone reductase subunit F in PDB entry 8a1v, assembly 1, front view.
Na(+)-translocating NADH-quinone reductase subunit F in PDB entry 8a1v, assembly 1, side view.
Na(+)-translocating NADH-quinone reductase subunit F in PDB entry 8a1v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A5F5Y4  
140850100150200250300350400
 
100200300400MSTIIFGVVMFTLIILALVLVILFAKSKLVPTGDITISINGDPEKAIVTQPGGKLLTALAGAGVFVSSACGGGGSCGQCRVKIKSGGGDILPTELDHISKGEAREGERLACQVAVKADMDLELPEEIFGVKKWECTVISNDNKATFIKELKLAIPDGESVPFRAGGYIQIEAPAHHVKYADFDVPEKYRGDWDKFNLFRYESKVDEPIIRAYSMANYPEEFGIIMLNVRIATPPPNNPNVPPGQMSSYIWSLKAGDKCTISGPFGEFFAKDTDAEMVFIGGGAGMAPMRSHIFDQLKRLKSKRKMSYWYGARSKREMFYVEDFDGLAAENDNFVWHCALSDPQPEDNWTGYTGFIHNVLYENYLKDHEAPEDCEYYMCGPPMMNAAVINMLKNLGVEEENILLDDFGG
UniProt
A5F5Y4
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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