6HUM | pdb_00006hum

Structure of the photosynthetic complex I from Thermosynechococcus elongatus


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth C]SCOP2 FamilyNADH-ubiquinone oxidoreductase chain 3-like 8067560 4005842 SCOP2 (2022-06-29)
B [auth C]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8106707 3002200 SCOP2 (2022-06-29)
C [auth D]SCOP2 FamilyND4 antiporter-like subunits 8059299 4005749 SCOP2 (2022-06-29)
C [auth D]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8093348 3002280 SCOP2 (2022-06-29)
C [auth D]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8059300 3002280 SCOP2 (2022-06-29)
D [auth E]SCOP2 FamilyNADH-quinone oxidoreductase NDH subunit 11-like 8060882 4005793 SCOP2 (2022-06-29)
D [auth E]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8060883 3002200 SCOP2 (2022-06-29)
I [auth H]SCOP2 FamilyNqo4-like 8085740 4000433 SCOP2 (2022-06-29)
I [auth H]SCOP2 SuperfamilyHydB/Nqo4-like 8085741 3001849 SCOP2 (2022-06-29)
M [auth F]SCOP2 FamilyND5 antiporter-like subunits 8059303 4005931 SCOP2 (2022-06-29)
M [auth F]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8059304 3002280 SCOP2 (2022-06-29)
M [auth F]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8093351 3002280 SCOP2 (2022-06-29)
P [auth S]SCOP2B SuperfamilyElectron transport accessory proteins 8103000 3000325 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ANADHdhe6humA1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit 8 (Nqo8)-relatedF: NADHdhECOD (1.6)
B [auth C]Oxidored_q4e6humC1 A: extended segmentsX: NADH-quinone oxidoreductase subunit A (From Topology)H: NADH-quinone oxidoreductase subunit A (From Topology)T: NADH-quinone oxidoreductase subunit AF: Oxidored_q4ECOD (1.6)
C [auth D]Proton_antipo_Me6humD1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit L (NuoL)-relatedF: Proton_antipo_MECOD (1.6)
D [auth E]Oxidored_q2e6humE1 A: alpha complex topologyX: NADH-quinone oxidoreductase subunit K (From Topology)H: NADH-quinone oxidoreductase subunit K (From Topology)T: NADH-quinone oxidoreductase subunit KF: Oxidored_q2ECOD (1.6)
E [auth B]Proton_antipo_Me6humB1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit L (NuoL)-relatedF: Proton_antipo_MECOD (1.6)
F [auth G]Oxidored_q3e6humG1 A: extended segmentsX: NADH-quinone oxidoreductase subunit J (From Topology)H: NADH-quinone oxidoreductase subunit J (From Topology)T: NADH-quinone oxidoreductase subunit JF: Oxidored_q3ECOD (1.6)
G [auth J]Complex1_30kDae6humJ1 A: a+b two layersX: Nqo5-likeH: Nqo5-like (From Topology)T: Nqo5-likeF: Complex1_30kDaECOD (1.6)
I [auth H]Complex1_49kDa_1ste6humH2 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: Complex1_49kDa_1stECOD (1.6)
I [auth H]NuoDe6humH1 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NuoDECOD (1.6)
I [auth H]Complex1_49kDa_2nde6humH3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: Complex1_49kDa_2ndECOD (1.6)
M [auth F]Proton_antipo_Me6humF1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit L (NuoL)-relatedF: Proton_antipo_MECOD (1.6)
P [auth S]NdhSe6humS1 A: beta barrelsX: SH3H: SH3T: SH3F: NdhSECOD (1.6)
Q [auth O]UNK_F_TYPEe6humO1 A: beta barrelsX: SH3H: SH3T: SH3F: UNK_F_TYPEECOD (1.6)
J [auth I]Fer4_21_1e6humI1 A: a+b two layersX: 4Fe-4S ferredoxin (From Topology)H: 4Fe-4S ferredoxin (From Topology)T: 4Fe-4S ferredoxinF: Fer4_21_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
B [auth C]PF00507NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 (Oxidored_q4)NADH-ubiquinone/plastoquinone oxidoreductase, chain 3- Family
C [auth D]PF00361NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)NADH:quinone oxidoreductase/Mrp antiporter, TMThis entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].
Domain
D [auth E]PF00420NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)NADH-ubiquinone/plastoquinone oxidoreductase chain 4L- Family
E [auth B]PF00361NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)NADH:quinone oxidoreductase/Mrp antiporter, TMThis entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].
Domain
F [auth G]PF00499NADH-ubiquinone/plastoquinone oxidoreductase chain 6 (Oxidored_q3)NADH-ubiquinone/plastoquinone oxidoreductase chain 6- Family
G [auth J]PF00329Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)Respiratory-chain NADH dehydrogenase, 30 Kd subunitDomain
I [auth H]PF00346Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)Respiratory-chain NADH dehydrogenase, 49 Kd subunit- Family
PF01058NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)NADH ubiquinone oxidoreductase, 20 Kd subunitDomain
PF10716NADH dehydrogenase transmembrane subunit (NdhL)NADH dehydrogenase transmembrane subunit- Family
M [auth F]PF00361NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)NADH:quinone oxidoreductase/Mrp antiporter, TMThis entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].
Domain
M [auth F]PF01010NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus (Proton_antipo_C)NADH-dehyrogenase subunit F, TMs, (complex I) C-terminusThis entry represents a carboxyl terminal extension of Pfam:PF00361. It includes subunit 5 from chloroplasts, and bacterial subunit L. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a re ...This entry represents a carboxyl terminal extension of Pfam:PF00361. It includes subunit 5 from chloroplasts, and bacterial subunit L. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. This family is largely a few TM regions of the F subunit of NADH-Ubiquinone oxidoreductase from plants. The TMs form part of the anti-porter subunit.
Domain
M [auth F]PF00662NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus (Proton_antipo_N)NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminusThis entry represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in ...This entry represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.
Domain
O [auth M]PF10664Cyanobacterial and plastid NDH-1 subunit M (NdhM)Cyanobacterial and plastid NDH-1 subunit MThe proton-pumping NADH:ubiquinone oxidoreductase catalyses the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and ...The proton-pumping NADH:ubiquinone oxidoreductase catalyses the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 sub-complexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit [1]. The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organisms [2]. The three subunits of NDH-1, NdhM, NdhN and NdhO are essential for effecting cyclic electron flow around photosystem I, by supplying extra-ATP for photosynthesis in both plastids and cyanobacteria [3, 4].
Domain
P [auth S]PF11623NAD(P)H dehydrogenase subunit S (NdhS)NAD(P)H dehydrogenase subunit S- Family
Q [auth O]PF11910Cyanobacterial and plant NDH-1 subunit O (NdhO)Cyanobacterial and plant NDH-1 subunit O- Family
J [auth I]PF128384Fe-4S dicluster domain (Fer4_7)4Fe-4S dicluster domainSuperfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
NAD(P)H-quinone oxidoreductase subunit 1
B [auth C]NAD(P)H-quinone oxidoreductase subunit 3
C [auth D]NAD(P)H-quinone oxidoreductase chain 4 1
D [auth E]NAD(P)H-quinone oxidoreductase subunit 4L
E [auth B]NAD(P)H-quinone oxidoreductase subunit 2
F [auth G]NADH dehydrogenase subunit 6 -
G [auth J]NAD(P)H-quinone oxidoreductase subunit J
H [auth P]Proton-translocating NADH-quinone dehydrogenase subunit P NdhP---
I [auth H]NAD(P)H-quinone oxidoreductase subunit H
NAD(P)H-quinone oxidoreductase subunit K
NAD(P)H-quinone oxidoreductase subunit L -
M [auth F]NADH dehydrogenase subunit 5
NAD(P)H-quinone oxidoreductase subunit N -
O [auth M]NAD(P)H-quinone oxidoreductase subunit M -
P [auth S]Tlr0636 protein- -
Q [auth O]NAD(P)H-quinone oxidoreductase subunit O -
R [auth Q]Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ---
J [auth I]NAD(P)H-quinone oxidoreductase subunit I

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
IPR018086NADH:ubiquinone oxidoreductase, subunit 1, conserved siteConserved Site
B [auth C]IPR023043NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastidFamily
B [auth C]IPR000440NADH:ubiquinone/plastoquinone oxidoreductase, chain 3Family
B [auth C]IPR038430NADH:ubiquinone oxidoreductase, subunit 3 superfamilyHomologous Superfamily
C [auth D]IPR022997NADH-quinone oxidoreductase chain 4Family
C [auth D]IPR003918NADH:ubiquinone oxidoreductaseFamily
C [auth D]IPR010227NADH-quinone oxidoreductase, chain M/4Family
C [auth D]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
D [auth E]IPR001133NADH-ubiquinone oxidoreductase chain 4L/KFamily
D [auth E]IPR039428NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-likeFamily
E [auth B]IPR010096NAD(P)H-quinone oxidoreductase, subunit N/subunit 2Family
E [auth B]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
E [auth B]IPR045693NAD(P)H-quinone oxidoreductase subunit 2, N-terminalDomain
F [auth G]IPR042106NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJHomologous Superfamily
F [auth G]IPR001457NADH:ubiquinone/plastoquinone oxidoreductase, chain 6Family
G [auth J]IPR037232NADH:ubiquinone oxidoreductase, 30kDa subunit superfamilyHomologous Superfamily
G [auth J]IPR001268NADH:ubiquinone oxidoreductase, 30kDa subunitDomain
G [auth J]IPR020396NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved siteConserved Site
G [auth J]IPR010218NADH dehydrogenase, subunit CFamily
I [auth H]IPR022885NAD(P)H-quinone oxidoreductase subunit D/HFamily
I [auth H]IPR014029NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved siteConserved Site
I [auth H]IPR029014[NiFe]-hydrogenase, large subunitHomologous Superfamily
I [auth H]IPR001135NADH-quinone oxidoreductase, subunit DDomain
IPR006138NADH-ubiquinone oxidoreductase, 20 Kd subunitFamily
IPR006137NADH:ubiquinone oxidoreductase-like, 20kDa subunitDomain
IPR019654NAD(P)H-quinone oxidoreductase subunit LFamily
M [auth F]IPR003945NADH-quinone oxidoreductase, chain 5-likeFamily
M [auth F]IPR002128NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminalDomain
M [auth F]IPR001516NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminalDomain
M [auth F]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
M [auth F]IPR018393NADH-plastoquinone oxidoreductase, chain 5 subgroupFamily
IPR020874NAD(P)H-quinone oxidoreductase, subunit NFamily
O [auth M]IPR018922NAD(P)H-quinone oxidoreductase subunit MFamily
P [auth S]IPR021659NADH dehydrogenase-like complex, subunit SFamily
Q [auth O]IPR020905NAD(P)H-quinone oxidoreductase subunit OFamily
J [auth I]IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
J [auth I]IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
J [auth I]IPR004497NAD(P)H-quinone oxidoreductase subunit IFamily
J [auth I]IPR010226NADH-quinone oxidoreductase, chain IFamily