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- PDB-3m9s: Crystal structure of respiratory complex I from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 3m9s
TitleCrystal structure of respiratory complex I from Thermus thermophilus
Components
  • (NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 12
  • NADH-quinone oxidoreductase subunits 7, 10 and 11NADH dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / COMPLEX I / ELECTRON TRANSPORT / RESPIRATORY CHAIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / 2 iron, 2 sulfur cluster binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain ...NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Cro/C1-type helix-turn-helix domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / 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. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / 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 / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 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 / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsEfremov, R.G. / Baradaran, R. / Sazanov, L.A.
CitationJournal: Nature / Year: 2010
Title: The architecture of respiratory complex I
Authors: Efremov, R.G. / Baradaran, R. / Sazanov, L.A.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit C
6: NADH-quinone oxidoreductase subunit B
9: NADH-quinone oxidoreductase subunit I
7: NADH-quinone oxidoreductase subunit 15
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
R: NADH-quinone oxidoreductase subunits 7, 10 and 11
H: NADH-quinone oxidoreductase subunit 8
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit C
F: NADH-quinone oxidoreductase subunit B
G: NADH-quinone oxidoreductase subunit I
J: NADH-quinone oxidoreductase subunit 15
O: NADH-quinone oxidoreductase subunit 12
P: NADH-quinone oxidoreductase subunit 13
Q: NADH-quinone oxidoreductase subunit 14
S: NADH-quinone oxidoreductase subunits 7, 10 and 11
T: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)857,54746
Polymers851,00826
Non-polymers6,53920
Water0
1
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit C
6: NADH-quinone oxidoreductase subunit B
9: NADH-quinone oxidoreductase subunit I
7: NADH-quinone oxidoreductase subunit 15
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
R: NADH-quinone oxidoreductase subunits 7, 10 and 11
H: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,77323
Polymers425,50413
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37540 Å2
ΔGint-337 kcal/mol
Surface area82150 Å2
2
A: NADH-quinone oxidoreductase subunit 1
B: NADH-quinone oxidoreductase subunit 2
C: NADH-quinone oxidoreductase subunit 3
D: NADH-quinone oxidoreductase subunit 4
E: NADH-quinone oxidoreductase subunit C
F: NADH-quinone oxidoreductase subunit B
G: NADH-quinone oxidoreductase subunit I
J: NADH-quinone oxidoreductase subunit 15
O: NADH-quinone oxidoreductase subunit 12
P: NADH-quinone oxidoreductase subunit 13
Q: NADH-quinone oxidoreductase subunit 14
S: NADH-quinone oxidoreductase subunits 7, 10 and 11
T: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,77323
Polymers425,50413
Non-polymers3,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37540 Å2
ΔGint-337 kcal/mol
Surface area82160 Å2
Unit cell
Length a, b, c (Å)96.390, 336.090, 262.240
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly (complex I) consists of chains 1,2,3,4,5,6,7,8,9,L,M,N,R and H. / The identical biological assembly in ASU consists of chains A,B,C,D,E,F,J,I,G,O,P,Q,S and T.

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Components

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NADH-quinone oxidoreductase subunit ... , 12 types, 24 molecules 1A2B3C4D5E6F9G7JLOMPNQHT

#1: Protein NADH-quinone oxidoreductase subunit 1 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 1 / NDH-1 subunit 1


Mass: 48693.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56222, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit 2 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 2 / NDH-1 subunit 2


Mass: 20309.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56221, NADH dehydrogenase (quinone)
#3: Protein NADH-quinone oxidoreductase subunit 3 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 3 / NDH-1 subunit 3


Mass: 86656.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56223, NADH dehydrogenase (quinone)
#4: Protein NADH-quinone oxidoreductase subunit 4 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 4 / NDH-1 subunit 4


Mass: 46428.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56220, NADH dehydrogenase (quinone)
#5: Protein NADH-quinone oxidoreductase subunit C / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit C / NDH-1 subunit 5


Mass: 23893.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56219, NADH dehydrogenase (quinone)
#6: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit B / NDH-1 subunit 6


Mass: 20262.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56218, NADH dehydrogenase (quinone)
#7: Protein NADH-quinone oxidoreductase subunit I / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit I / NDH-1 subunit 9


Mass: 20106.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q56224, NADH dehydrogenase (quinone)
#8: Protein NADH-quinone oxidoreductase subunit 15 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 15 / NDH-1 subunit 15


Mass: 14812.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKZ7, NADH dehydrogenase (quinone)
#9: Protein NADH-quinone oxidoreductase subunit 12 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 12 / NDH-1 subunit 12


Mass: 39932.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: NADH dehydrogenase (quinone)
#10: Protein NADH-quinone oxidoreductase subunit 13 / NADH dehydrogenase (quinone)


Mass: 33379.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-quinone oxidoreductase subunit 14 / NADH dehydrogenase (quinone)


Mass: 32272.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-quinone oxidoreductase subunit 8 / NADH dehydrogenase (quinone)


Mass: 15421.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: NADH:ubiquinone reductase (H+-translocating)

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Protein , 1 types, 2 molecules RS

#12: Protein NADH-quinone oxidoreductase subunits 7, 10 and 11 / NADH dehydrogenase (quinone)


Mass: 23336.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 3 types, 20 molecules

#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#16: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Compound detailsTHE LONG C-N BONDS ARE BECAUSE OF THE LOOPS NOT BEING MODELED.
Sequence detailsTHE ACTUAL SEQUENCE FOR CHAIN L,O: MALLGTILLPLLGFALLGLFGKRMREPLPGVLASGLVLASFLLGAGLLLSGGARFQAEWL ...THE ACTUAL SEQUENCE FOR CHAIN L,O: MALLGTILLPLLGFALLGLFGKRMREPLPGVLASGLVLASFLLGAGLLLSGGARFQAEWL PGIPFSLLLDNLSGFMLLIVTGVGFLIHVYAIGYMGGDPGYSRFFAYFNLFIAMMLTLVL ADSYPVMFIGWEGVGLASFLLIGFWYKNPQYADSARKAFIVNRIGDLGFMLGMAILWALY GTLSISELKEAMEGPLKNPDLLALAGLLLFLGAVGKSAQIPLMVWLPDAMAGPTPVSALI HAATMVTAGVYLIARSSFLYSVLPDVSYAIAVVGLLTAAYGALSAFGQTDIKKIVAYSTI SQLGYMFLAAGVGAYWVALFHVFTHAFFKALLFLASGSVIHALGGEQDVRKMGGLWKHLP QTRWHALIGALALGGLPLLSGFWSKDAILAATLTYPFGGVGFYVGALLVAVLTAMYAMRW FVLVFLGEERGHHHPHEAPPVMLWPNHLLALGSVLAGYLALPHPLPNVLEPFLKPALAEV EAHHLSLGAEWGLIALSAAVALLGLWAGFVFFQRKVFPAWYLAFEAASREAFYVDRAYNA LIVNPLKALAEALFYGDRGLLSGYFGLGGAARSLGQGLARLQTGYLRVYALLFVLGALLLLGVMRW THE ACTUAL SEQUENCE FOR CHAIN M,P: MVVLAVLLPVVFGALLLLGLPRALGVLGAGLSFLLNLYLFLTHPGGVAHAFQAPLLPGAG VYWAFGLDGLSALFFLTIALTVFLGALVARVEGRFLGLALLMEGLLLGLFAARDLLVFYV FFEAALIPALLMLYLYGGEGRTRALYTFVLFTLVGSLPMLAAVLGDRLLSGSPTFLLEDL LAHPLQEEAAFWVFLGFALAFDIKTPLFPLHAWLPPFHQENHPSGLADALGTLYKVGVFD FFRFDIPLAPEGFAQAQGLLLFLAALSALYGAWVAFAAKDFKTLLAYAGLSHMGVAALGV FSGTPEGAMGGLYLLAASGVYTGGLFLLAGRLYERTGTLEIGRYRGLAQSAPGLAALALI LFLAMVGLPGLSGFPGEFLTLLGAYKASPWLAALAFLSVIASAAYALTAFQKTFWEEGGS GVKDLAGAEWGFALLSVLALLLMGVFPGYFARGLHPLAEAFAKLLGGGA THE ACTUAL SEQUENCE FOR CHAIN N,Q: MTLAILAVFSVALTLLGFVLPPQGVKRATLLGLALALASLLLTWGKPFAFGPYAVDGVSQ VFTLLALLGALWTVGLVRSGGFEFYLLVLYAALGMHLLASTRHLLLMLVALEALSLPLYA LATWRRGQGLEAALKYFLLGALAAAFFLYGAALFYGDTGSLVLGAPGEGPLYALALGLLL VGLGFKAALAPFHFWTPDVYQGSPTPVVLFMATSVKAAAFAALLRVAAPPEAVALLVALS VVVGNLAALAQKEAKRLLAYSSIAHAGYMALALYTGNAQALGFYLLTYVLATGLAFAVLS QISPDRVPLEALRGLYRKDPLLGLAFLVAMLSLLGLPPLAGFWGKYLAFAEAARAGAWGV LVLALVTSAVSAYYYLGLGLAVFARPEETPFRPGPPWARAAVVAAGSSSSPWGSSPASSS PPWPRGVKITP THE ACTUAL SEQUENCE FOR CHAIN R,S: MAPIQEYVGTLIYVGVALFIGVAALLVGALLGPKKPGRAKLMPYESGNDPAGEVKRFPVH FYVVAMLFILFDVEVAFLWPYAVSAGGLGLYGFLGVLAFTLLLFVGFLYEWWKGVMRWH MSLLEGLALFLLLLSGVLVVTLRNAIHAALALILNFLVLAGVYVALDARFLGFIQVIVYA GAIVVLFLFVIMLLFAAQGEIGFDPLVRSRPLAALLALGVAGILAAGLWGLDLAFTQDLK GGLPQALGPLLYGDWLFVLLAVGFLLMAATVVAVALVEPGKASRAKEAEKREEVAR MSYLLTSALLFALGVYGVLTRRTAILVFLSIELMLNAANLSLVGFARAYGLDGQVAALMV IAVAAAEVAVGLGLIVAIFRHRESTAVDDLSELRG THE ACTUAL SEQUENCE FOR CHAIN H,T: MTWSYPVDPYWMVALKALLVVVGLLTAFAFMTLIERRLLARFQVRMGPNRVGPFGLLQPL ADAIKSIFKEDIVVAQADRFLFVLAPLISVVFALLAFGLIPFGPPGSFFGYQPWVINLDL GILYLFAVSELAVYGIFLSGWASGSKYSLLGSLRSSASLISYELGLGLALLAPVLLVGSL NLNDIVNWQKEHGWLFLYAFPAFLVYLIASMAEAARTPFDLPEAEQELVGGYHTEYSSIK WALFQMAEYIHFITASALIPTLFLGGWTMPVLEVPYLWMFLKIAFFLFFFIWIRATWFRL RYDQLLRFGWGFLFPLALLWFLVTALVVALDLPRTYLLYLSALSFLVLLGAVLYTPKPARKGGGA

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.91 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 16% PEG 4000, 100 mM Bis-Tris, 100 mM KCl, 100 mM glutaric acid and 2.04 mM n-octyl- -maltoside fluorinated, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→30 Å / Num. all: 72549 / Num. obs: 72549 / % possible obs: 74.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 132.9 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 2.5
Reflection shellResolution: 4.5→4.74 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1 / Num. unique all: 9162 / % possible all: 65.1

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Processing

Software
NameClassification
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3I9V AND 3M9C

3i9v

3m9c


Resolution: 4.5→30 Å / Num. reflection all: 72549 / Num. reflection obs: 72549
Details: The structure is not refined and consists of the atomic molecular replacement model of the hydrophilic domain and the backbone alpha-helical model of the membrane domain. Reflection data was ...Details: The structure is not refined and consists of the atomic molecular replacement model of the hydrophilic domain and the backbone alpha-helical model of the membrane domain. Reflection data was anisotropically scaled, for optimal electron density calculation. The directionality of the helices in the membrane domain is not known. The crystal is twinned (twin law "-h, -k, h+l"), with twin fraction 0.46.
Refinement stepCycle: LAST / Resolution: 4.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47474 0 190 0 47664

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