Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL
Hirata, K., Tsukihara, T., Ago, H.(2014) Nature Methods 11: 734-736
- DOI: https://doi.org/10.1038/NMETH.2962
Experimental Data Snapshot
(2014) Nature Methods 11: 734-736
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 1 | 514 | Bos taurus | Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00396 (Bos taurus) Explore P00396  Go to UniProtKB:  P00396 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00396 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 2 | 227 | Bos taurus | Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P68530 (Bos taurus) Explore P68530  Go to UniProtKB:  P68530 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P68530 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 3 | 261 | Bos taurus | Mutation(s): 0  EC: 7.1.1.9 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00415 (Bos taurus) Explore P00415  Go to UniProtKB:  P00415 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00415 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 4 isoform 1 | 147 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00423 (Bos taurus) Explore P00423  Go to UniProtKB:  P00423 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00423 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 5A | 109 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00426 (Bos taurus) Explore P00426  Go to UniProtKB:  P00426 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00426 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 5B, mitochondrial | 98 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00428 (Bos taurus) Explore P00428  Go to UniProtKB:  P00428 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00428 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 6A2 | 85 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P07471 (Bos taurus) Explore P07471  Go to UniProtKB:  P07471 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07471 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 6B1 | 85 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00429 (Bos taurus) Explore P00429  Go to UniProtKB:  P00429 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00429 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 6C | 73 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P04038 (Bos taurus) Explore P04038  Go to UniProtKB:  P04038 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04038 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 7A1 | 59 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P07470 (Bos taurus) Explore P07470  Go to UniProtKB:  P07470 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07470 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 11 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 7B | 56 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P13183 (Bos taurus) Explore P13183  Go to UniProtKB:  P13183 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P13183 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 12 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 7C, mitochondrial | 47 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P00430 (Bos taurus) Explore P00430  Go to UniProtKB:  P00430 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00430 | ||||
Sequence AnnotationsExpand | |||||
|
Entity ID: 13 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cytochrome c oxidase subunit 8B | 46 | Bos taurus | Mutation(s): 0  Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P10175 (Bos taurus) Explore P10175  Go to UniProtKB:  P10175 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P10175 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 16 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CDL Query on CDL | KE [auth T], ND [auth P], PB [auth G], ZA [auth C] | CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L | |||
TGL Query on TGL | CC [auth L] DD [auth O] IB [auth D] QA [auth B] VE [auth Y] | TRISTEAROYLGLYCEROL C57 H110 O6 DCXXMTOCNZCJGO-UHFFFAOYSA-N | |||
HEA Query on HEA | AA [auth A], BA [auth A], JC [auth N], KC [auth N] | HEME-A C49 H56 Fe N4 O6 ZGGYGTCPXNDTRV-PRYGPKJJSA-L | |||
PEK Query on PEK | CB [auth C] EB [auth C] LD [auth P] QB [auth G] QD [auth P] | (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C43 H78 N O8 P ANRKEHNWXKCXDB-BHFWLYLHSA-N | |||
PSC Query on PSC | QC [auth N], SA [auth B] | (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C42 H81 N O8 P JLPULHDHAOZNQI-AUSZDXHESA-O | |||
PGV Query on PGV | DB [auth C] GA [auth A] HA [auth A] ID [auth P] JD [auth P] | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C40 H77 O10 P ADYWCMPUNIVOEA-GPJPVTGXSA-N | |||
DMU Query on DMU | AC [auth K] AE [auth Q] BC [auth K] DC [auth L] HB [auth C] | DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N | |||
CHD Query on CHD | AB [auth C] BB [auth C] EC [auth L] JE [auth T] NE [auth W] | CHOLIC ACID C24 H40 O5 BHQCQFFYRZLCQQ-OELDTZBJSA-N | |||
CUA Query on CUA | ED [auth O], RA [auth B] | DINUCLEAR COPPER ION Cu2 ALKZAGKDWUSJED-UHFFFAOYSA-N | |||
PO4 Query on PO4 | ME [auth U], UB [auth H] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
ZN Query on ZN | CE [auth S], KB [auth F] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CU Query on CU | CA [auth A], LC [auth N] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N | |||
EDO Query on EDO | AD [auth N] BD [auth N] BE [auth R] CD [auth N] DE [auth S] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
PER Query on PER | FA [auth A], OC [auth N] | PEROXIDE ION O2 ANAIPYUSIMHBEL-UHFFFAOYSA-N | |||
MG Query on MG | DA [auth A], MC [auth N] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | EA [auth A], KD [auth P], NC [auth N], WA [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Modified Residues 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
FME Query on FME | A, N | L-PEPTIDE LINKING | C6 H11 N O3 S | MET | |
TPO Query on TPO | G, T | L-PEPTIDE LINKING | C4 H10 N O6 P | THR | |
SAC Query on SAC | I, V | L-PEPTIDE LINKING | C5 H9 N O4 | SER |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 182.6 | α = 90 |
b = 204.51 | β = 90 |
c = 178.29 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
Funding Organization | Location | Grant Number |
---|---|---|
Japan Society for the Promotion of Science (JSPS) | Japan | 18K06092 |