3WG7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

PDB DOI: https://doi.org/10.2210/pdb3WG7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2013-07-29 Released: 2014-04-30
Deposition Author(s): Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.195
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

PubMed: 24813624 Search on PubMed
DOI: https://doi.org/10.1038/nmeth.2962
Primary Citation of Related Structures:
3WG7

PubMed Abstract:
We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

Organizational Affiliation

1] RIKEN SPring-8 Center, Sayo, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan. [3].

Macromolecule Content

Total Structure Weight: 441.9 kDa
Atom Count: 33,302
Modelled Residue Count: 3,558
Deposited Residue Count: 3,614
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00396
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68530
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	261	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00415
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D, Q	147	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00423
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E, R	109	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
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UniProt Group	P00426
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
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UniProt Group	P00428
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	G, T	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
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UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
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UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
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UniProt Group	P04038
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	J, W	59	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
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UniProt Group	P07470
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	K, X	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
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UniProt Group	P13183
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	47	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00430
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	M, Z	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10175
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Reference Sequence

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain RB [auth P] SDF format, chain WA [auth G] SDF format, chain YB [auth T] MOL2 format, chain PA [auth C] MOL2 format, chain RB [auth P] MOL2 format, chain WA [auth G] MOL2 format, chain YB [auth T]	PA [auth C], RB [auth P], WA [auth G], YB [auth T]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain PA [auth C] Focus chain RB [auth P] Focus chain WA [auth G] Focus chain YB [auth T] Interactions & Density Focus chain PA [auth C] Focus chain RB [auth P] Focus chain WA [auth G] Focus chain YB [auth T]
TGL Query on TGL Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain AB [auth L] SDF format, chain AC [auth Y] SDF format, chain KB [auth N] SDF format, chain UA [auth D] SDF format, chain VB [auth Q] MOL2 format, chain IA [auth B] MOL2 format, chain AB [auth L] MOL2 format, chain AC [auth Y] MOL2 format, chain KB [auth N] MOL2 format, chain UA [auth D] MOL2 format, chain VB [auth Q]	AB [auth L] AC [auth Y] IA [auth B] KB [auth N] UA [auth D] AB [auth L], AC [auth Y], IA [auth B], KB [auth N], UA [auth D], VB [auth Q]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain IA [auth B] Focus chain KB [auth N] Focus chain UA [auth D] Focus chain VB [auth Q] Interactions & Density Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain IA [auth B] Focus chain KB [auth N] Focus chain UA [auth D] Focus chain VB [auth Q]
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CB [auth N] SDF format, chain DB [auth N] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth N] MOL2 format, chain DB [auth N]	AA [auth A], BA [auth A], CB [auth N], DB [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth N] Focus chain DB [auth N] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth N] Focus chain DB [auth N]
PEK Query on PEK Download Ideal Coordinates CCD File SDF format, chain SA [auth C] SDF format, chain NA [auth C] SDF format, chain PB [auth P] SDF format, chain UB [auth P] SDF format, chain XA [auth G] SDF format, chain XB [auth T] MOL2 format, chain SA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain PB [auth P] MOL2 format, chain UB [auth P] MOL2 format, chain XA [auth G] MOL2 format, chain XB [auth T]	NA [auth C] PB [auth P] SA [auth C] UB [auth P] XA [auth G] NA [auth C], PB [auth P], SA [auth C], UB [auth P], XA [auth G], XB [auth T]	(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		Interactions Focus chain NA [auth C] Focus chain PB [auth P] Focus chain SA [auth C] Focus chain UB [auth P] Focus chain XA [auth G] Focus chain XB [auth T] Interactions & Density Focus chain NA [auth C] Focus chain PB [auth P] Focus chain SA [auth C] Focus chain UB [auth P] Focus chain XA [auth G] Focus chain XB [auth T]
PSC Query on PSC Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain LB [auth N] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth N]	LA [auth B], LB [auth N]	(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		Interactions Focus chain LA [auth B] Focus chain LB [auth N] Interactions & Density Focus chain LA [auth B] Focus chain LB [auth N]
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain JB [auth N] SDF format, chain QB [auth P] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IB [auth N] SDF format, chain NB [auth P] SDF format, chain OA [auth C] SDF format, chain TA [auth C] MOL2 format, chain JB [auth N] MOL2 format, chain QB [auth P] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IB [auth N] MOL2 format, chain NB [auth P] MOL2 format, chain OA [auth C] MOL2 format, chain TA [auth C]	GA [auth A] HA [auth A] IB [auth N] JB [auth N] NB [auth P] GA [auth A], HA [auth A], IB [auth N], JB [auth N], NB [auth P], OA [auth C], QB [auth P], TA [auth C]	(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		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IB [auth N] Focus chain JB [auth N] Focus chain NB [auth P] Focus chain OA [auth C] Focus chain QB [auth P] Focus chain TA [auth C] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IB [auth N] Focus chain JB [auth N] Focus chain NB [auth P] Focus chain OA [auth C] Focus chain QB [auth P] Focus chain TA [auth C]
DMU Query on DMU Download Ideal Coordinates CCD File SDF format, chain BB [auth M] SDF format, chain BC [auth Z] MOL2 format, chain BB [auth M] MOL2 format, chain BC [auth Z]	BB [auth M], BC [auth Z]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain BB [auth M] Focus chain BC [auth Z] Interactions & Density Focus chain BB [auth M] Focus chain BC [auth Z]
CHD Query on CHD Download Ideal Coordinates CCD File SDF format, chain SB [auth P] SDF format, chain TB [auth P] SDF format, chain KA [auth B] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain YA [auth G] SDF format, chain ZA [auth J] SDF format, chain ZB [auth W] MOL2 format, chain SB [auth P] MOL2 format, chain TB [auth P] MOL2 format, chain KA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth J] MOL2 format, chain ZB [auth W]	KA [auth B] QA [auth C] RA [auth C] SB [auth P] TB [auth P] KA [auth B], QA [auth C], RA [auth C], SB [auth P], TB [auth P], YA [auth G], ZA [auth J], ZB [auth W]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain KA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth P] Focus chain TB [auth P] Focus chain YA [auth G] Focus chain ZA [auth J] Focus chain ZB [auth W] Interactions & Density Focus chain KA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth P] Focus chain TB [auth P] Focus chain YA [auth G] Focus chain ZA [auth J] Focus chain ZB [auth W]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain MB [auth O] SDF format, chain JA [auth B] MOL2 format, chain MB [auth O] MOL2 format, chain JA [auth B]	JA [auth B], MB [auth O]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain MB [auth O] Interactions & Density Focus chain JA [auth B] Focus chain MB [auth O]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain VA [auth F] SDF format, chain WB [auth S] MOL2 format, chain VA [auth F] MOL2 format, chain WB [auth S]	VA [auth F], WB [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain VA [auth F] Focus chain WB [auth S] Interactions & Density Focus chain VA [auth F] Focus chain WB [auth S]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain EB [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain EB [auth N]	CA [auth A], EB [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain EB [auth N] Interactions & Density Focus chain CA [auth A] Focus chain EB [auth N]
PER Query on PER Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain HB [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain HB [auth N]	FA [auth A], HB [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain HB [auth N] Interactions & Density Focus chain FA [auth A] Focus chain HB [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain FB [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain FB [auth N]	DA [auth A], FB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain FB [auth N] Interactions & Density Focus chain DA [auth A] Focus chain FB [auth N]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain EA [auth A] SDF format, chain GB [auth N] SDF format, chain OB [auth P] MOL2 format, chain MA [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain GB [auth N] MOL2 format, chain OB [auth P]	EA [auth A], GB [auth N], MA [auth C], OB [auth P]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GB [auth N] Focus chain MA [auth C] Focus chain OB [auth P] Interactions & Density Focus chain EA [auth A] Focus chain GB [auth N] Focus chain MA [auth C] Focus chain OB [auth P]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.195
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.6	α = 90
b = 204.51	β = 90
c = 178.29	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2014-06-25
Changes: Database references
Version 1.2: 2018-01-24
Changes: Data collection
Version 1.3: 2022-08-24
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-11-08
Changes: Data collection, Refinement description

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3WG7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

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