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- PDB-6tg9: Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate ... -

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Basic information

Entry
Database: PDB / ID: 6tg9
TitleCryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus
Components
  • (Formate dehydrogenase subunit ...) x 3
  • NAD-dependent formate dehydrogenase subunit delta
KeywordsOXIDOREDUCTASE / molybdoenzyme / formate oxidation / NAD+-dependent
Function / homology
Function and homology information


formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding ...formate dehydrogenase complex / formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain ...Formate dehydrogenase, delta subunit / NADH-dependant formate dehydrogenase delta subunit FdsD / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / 2Fe-2S iron-sulfur cluster binding domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Aspartate decarboxylase-like domain superfamily / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Formate dehydrogenase subunit beta / NAD-dependent formate dehydrogenase subunit delta / Formate dehydrogenase ...: / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Formate dehydrogenase subunit beta / NAD-dependent formate dehydrogenase subunit delta / Formate dehydrogenase / Formate dehydrogenase subunit gamma / NAD-dependent formate dehydrogenase, delta subunit / formate dehydrogenase / NAD-dependent formate dehydrogenase, beta subunit / NAD-dependent formate dehydrogenase, gamma subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsWendler, P. / Radon, C. / Mittelstaedt, G.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationEXC 314/2 Germany
German Research FoundationEXC 2008/1 Germany
European UnioniNext-4008 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.
Authors: Christin Radon / Gerd Mittelstädt / Benjamin R Duffus / Jörg Bürger / Tobias Hartmann / Thorsten Mielke / Christian Teutloff / Silke Leimkühler / Petra Wendler /
Abstract: Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor ...Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _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

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Formate dehydrogenase subunit alpha
B: Formate dehydrogenase subunit beta
G: Formate dehydrogenase subunit gamma
D: NAD-dependent formate dehydrogenase subunit delta
E: Formate dehydrogenase subunit alpha
F: Formate dehydrogenase subunit beta
C: Formate dehydrogenase subunit gamma
H: NAD-dependent formate dehydrogenase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,35934
Polymers360,6738
Non-polymers9,68626
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36680 Å2
ΔGint-473 kcal/mol
Surface area106170 Å2
MethodPISA

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Components

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Formate dehydrogenase subunit ... , 3 types, 6 molecules AEBFGC

#1: Protein Formate dehydrogenase subunit alpha /


Mass: 104589.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16550 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2PAE3, UniProt: D5AQH0*PLUS
#2: Protein Formate dehydrogenase subunit beta /


Mass: 52755.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16555 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2P9P2, UniProt: D5AQH1*PLUS
#3: Protein Formate dehydrogenase subunit gamma /


Mass: 15603.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16560 / Production host: Rhodobacter capsulatus (bacteria)
References: UniProt: A0A0E2PAI9, UniProt: D5AQH2*PLUS, formate dehydrogenase

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Protein , 1 types, 2 molecules DH

#4: Protein NAD-dependent formate dehydrogenase subunit delta


Mass: 7388.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: U715_16540 / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: A0A0E2P9Z0, UniProt: D5AQG8*PLUS

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Non-polymers , 7 types, 26 molecules

#5: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Formate dehydrogenase, NADH reduced / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.36 MDa / Experimental value: YES
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Source (recombinant)Organism: Rhodobacter capsulatus (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
175 mMpotassium phosphate1
210 mMsodium azide1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company /
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELDBright-field microscopy / Specimen-ID: 1

IDCryogenModel
1NITROGENFEI POLARA 300
2FEI TITAN KRIOS
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector model
1164SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)
2240GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1.10CTF correction
7Coot0.8model fitting
10IMAGICinitial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
14PHENIX1.14model refinement
CTF correctionDetails: CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199229 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11FDO

1fdo

11FDO1PDBexperimental model
23IAM

3iam

13IAM2PDBexperimental model
35XF9

5xf9

15XF93PDBexperimental model
RefinementHighest resolution: 3.24 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0150692
ELECTRON MICROSCOPYf_angle_d0.77591554
ELECTRON MICROSCOPYf_dihedral_angle_d14.25419946
ELECTRON MICROSCOPYf_chiral_restr0.0563968
ELECTRON MICROSCOPYf_plane_restr0.0037724

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