5B6Y

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation

> Summary

Summary for 5B6Y

Related5B6W 5B6V 5B6Y 5B6Z
DescriptorBacteriorhodopsin
Functional Keywordsbacteriorhodopsin, xfel, time-resolved serial femtosecond crystallography, sacla, proton transport
Biological sourceHalobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
Cellular locationCell membrane; Multi-pass membrane protein P02945
Total number of polymer chains1
Total molecular weight30891.94
Authors
Royant, A.,Nango, E.,Nakane, T.,Tanaka, T.,Arima, T.,Neutze, R.,Iwata, S. (deposition date: 2016-06-02, release date: 2016-12-21, Last modification date: 2017-02-01)
Primary citation
Nango, E.,Royant, A.,Kubo, M.,Nakane, T.,Wickstrand, C.,Kimura, T.,Tanaka, T.,Tono, K.,Song, C.,Tanaka, R.,Arima, T.,Yamashita, A.,Kobayashi, J.,Hosaka, T.,Mizohata, E.,Nogly, P.,Sugahara, M.,Nam, D.,Nomura, T.,Shimamura, T.,Im, D.,Fujiwara, T.,Yamanaka, Y.,Jeon, B.,Nishizawa, T.,Oda, K.,Fukuda, M.,Andersson, R.,Bath, P.,Dods, R.,Davidsson, J.,Matsuoka, S.,Kawatake, S.,Murata, M.,Nureki, O.,Owada, S.,Kameshima, T.,Hatsui, T.,Joti, Y.,Schertler, G.,Yabashi, M.,Bondar, A.N.,Standfuss, J.,Neutze, R.,Iwata, S.
A three-dimensional movie of structural changes in bacteriorhodopsin
Science, 354:1552-1557, 2016
PubMed: 28008064
DOI: 10.1126/science.aah3497
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.1 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.18030.4%015.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5b6y
no rotation
Molmil generated image of 5b6y
rotated about x axis by 90°
Molmil generated image of 5b6y
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5b6y
no rotation
Molmil generated image of 5b6y
rotated about x axis by 90°
Molmil generated image of 5b6y
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5b6y.pdb1.gz [296.1 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ABacteriorhodopsinpolymer24826814.41
UniProt (P02945)
Pfam (PF01036)
Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)BR,Bacterioopsin,BO
RETINALnon-polymer284.41
2,3-DI-PHYTANYL-GLYCEROLnon-polymer653.23
TRIDECANEnon-polymer184.41
DECANEnon-polymer142.31
HEPTANEnon-polymer100.21
N-OCTANEnon-polymer114.23
PENTADECANEnon-polymer212.42
UNDECANEnon-polymer156.32
nonanenon-polymer128.31
TETRADECANEnon-polymer198.41
waterwater18.021

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight26814.4
Non-Polymers*Number of molecules16
Total molecular weight4077.5
All*Total molecular weight30891.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.1 Å)

Cell axes62.50062.500112.000
Cell angles90.0090.00120.00
SpacegroupP 63
Resolution limits21.91 - 2.10
the highest resolution shell value2.262 - 2.100
R-factor0.1637
R-work0.16260
the highest resolution shell value0.225
R-free0.18190
the highest resolution shell value0.270
RMSD bond length0.003
RMSD bond angle0.812

Data Collection Statistics

Resolution limits39.92 - 2.10
the highest resolution shell value -
Number of reflections14513
Completeness100.0
Redundancy242

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1LIPIDIC CUBIC PHASE293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0016021cellular_componentintegral component of membrane
A0005886cellular_componentplasma membrane
A0005216molecular_functionion channel activity
A0009881molecular_functionphotoreceptor activity
A0007602biological_processphototransduction
A0018298biological_processprotein-chromophore linkage
A0015992biological_processproton transport
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC111binding site for residue RET A 300
ChainResidue
ATRP86
ATHR90
AMET118
ATRP138
ASER141
ATRP182
ATYR185
APRO186
AASP212
AALA215
ALYS216

AC26binding site for residue L2P A 600
ChainResidue
AALA44
ALEU48
APHE54
ATHR107
ATYR147
AD10602

AC32binding site for residue TRD A 601
ChainResidue
ALEU149
ASER183

AC43binding site for residue D10 A 602
ChainResidue
ALEU22
AL2P600
AHP6603

AC51binding site for residue HP6 A 603
ChainResidue
AD10602

AC62binding site for residue OCT A 604
ChainResidue
ALYS172
AASN176

AC71binding site for residue OCT A 605
ChainResidue
AMYS606

AC82binding site for residue MYS A 606
ChainResidue
AOCT605
AL2P608

AC91binding site for residue UND A 607
ChainResidue
AL2P608

AD15binding site for residue L2P A 608
ChainResidue
ATYR131
ATRP138
AILE203
AMYS606
AUND607

AD212binding site for residue L2P A 609
ChainResidue
AILE52
AMET56
ATYR64
ATRP80
AALA84
AGLY116
AILE117
AGLY120
ALEU123
ALEU123
AVAL124
AC14612

AD31binding site for residue MYS A 610
ChainResidue
ATYR26

AD41binding site for residue DD9 A 611
ChainResidue
AARG225

AD54binding site for residue C14 A 612
ChainResidue
ALEU87
APRO91
ALEU95
AL2P609

AD61binding site for residue OCT A 613
ChainResidue
ATYR26

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
HP6_5b6y_A_6036HEPTANE binding site
ChainResidueligand
AILE4HP6: HEPTANE
ATHR17HP6: HEPTANE
APHE54HP6: HEPTANE
ALEU58HP6: HEPTANE
ALEU61-LEU62HP6: HEPTANE

D10_5b6y_A_60210DECANE binding site
ChainResidueligand
ATRP10D10: DECANE
AALA14D10: DECANE
ATHR17-ALA18D10: DECANE
AGLY21-LEU22D10: DECANE
ALEU25D10: DECANE
APHE54D10: DECANE
ALEU58D10: DECANE
ALEU61D10: DECANE

MYS_5b6y_A_61010PENTADECANE binding site
ChainResidueligand
ALEU19MYS: PENTADECANE
ALEU22-GLY23MYS: PENTADECANE
ATYR26MYS: PENTADECANE
AVAL213-SER214MYS: PENTADECANE
AVAL217-GLY218MYS: PENTADECANE
ALEU221MYS: PENTADECANE
AARG225MYS: PENTADECANE

OCT_5b6y_A_6135N-OCTANE binding site
ChainResidueligand
ALEU22OCT: N-OCTANE
ALEU25-TYR26OCT: N-OCTANE
AVAL29-LYS30OCT: N-OCTANE

L2P_5b6y_A_609152,3-DI-PHYTANYL-GLYCEROL binding site
ChainResidueligand
ALEU48L2P: 2,3-DI-PHYTANYL-GLYCEROL
AILE52L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATHR55-MET56L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATYR64L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATHR67L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATRP80L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATYR83-ASP85L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU87-PHE88L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU92L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU123L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU127L2P: 2,3-DI-PHYTANYL-GLYCEROL

RET_5b6y_A_30027RETINAL binding site
ChainResidueligand
AVAL49RET: RETINAL
ATYR83RET: RETINAL
AASP85-TRP86RET: RETINAL
ATHR89-THR90RET: RETINAL
ALEU93RET: RETINAL
AMET118-ILE119RET: RETINAL
AGLY122-LEU123RET: RETINAL
ATRP137-TRP138RET: RETINAL
ASER141-THR142RET: RETINAL
AMET145RET: RETINAL
ATHR178RET: RETINAL
ALEU181-SER183RET: RETINAL
ATYR185-PRO186RET: RETINAL
ATRP189RET: RETINAL
APHE208RET: RETINAL
AASP212RET: RETINAL
AALA215-LYS216RET: RETINAL

C14_5b6y_A_61210TETRADECANE binding site
ChainResidueligand
ALEU87-PHE88C14: TETRADECANE
APRO91-LEU92C14: TETRADECANE
ALEU95C14: TETRADECANE
AGLN105C14: TETRADECANE
AILE108-LEU109C14: TETRADECANE
AVAL112C14: TETRADECANE
AGLY116C14: TETRADECANE

L2P_5b6y_A_600102,3-DI-PHYTANYL-GLYCEROL binding site
ChainResidueligand
AGLY106-THR107L2P: 2,3-DI-PHYTANYL-GLYCEROL
AALA110L2P: 2,3-DI-PHYTANYL-GLYCEROL
AGLY113-ALA114L2P: 2,3-DI-PHYTANYL-GLYCEROL
AILE117L2P: 2,3-DI-PHYTANYL-GLYCEROL
AILE140L2P: 2,3-DI-PHYTANYL-GLYCEROL
AALA143-ALA144L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATYR147L2P: 2,3-DI-PHYTANYL-GLYCEROL

UND_5b6y_A_6076UNDECANE binding site
ChainResidueligand
ATYR131-SER132UND: UNDECANE
APHE135-VAL136UND: UNDECANE
ATRP138-ALA139UND: UNDECANE

L2P_5b6y_A_608112,3-DI-PHYTANYL-GLYCEROL binding site
ChainResidueligand
ATYR131L2P: 2,3-DI-PHYTANYL-GLYCEROL
APHE135L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATRP138-ILE140L2P: 2,3-DI-PHYTANYL-GLYCEROL
ATHR142-ALA143L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU146L2P: 2,3-DI-PHYTANYL-GLYCEROL
ALEU190L2P: 2,3-DI-PHYTANYL-GLYCEROL
AGLY195-ALA196L2P: 2,3-DI-PHYTANYL-GLYCEROL

TRD_5b6y_A_60112TRIDECANE binding site
ChainResidueligand
ATRP138TRD: TRIDECANE
ATHR142TRD: TRIDECANE
AMET145-LEU146TRD: TRIDECANE
ALEU149-TYR150TRD: TRIDECANE
APHE153-PHE154TRD: TRIDECANE
AVAL179TRD: TRIDECANE
ASER183TRD: TRIDECANE
APRO186-VAL187TRD: TRIDECANE

UND_5b6y_A_6146UNDECANE binding site
ChainResidueligand
AALA143-ALA144UND: UNDECANE
ALEU146-TYR147UND: UNDECANE
ATYR150-VAL151UND: UNDECANE

OCT_5b6y_A_6056N-OCTANE binding site
ChainResidueligand
APHE153OCT: N-OCTANE
AVAL179-VAL180OCT: N-OCTANE
ASER183-ALA184OCT: N-OCTANE
AVAL187OCT: N-OCTANE

OCT_5b6y_A_6046N-OCTANE binding site
ChainResidueligand
ALYS172-VAL173OCT: N-OCTANE
AASN176-VAL177OCT: N-OCTANE
AVAL180-LEU181OCT: N-OCTANE

DD9_5b6y_A_6118nonane binding site
ChainResidueligand
AVAL177DD9: nonane
ALEU181DD9: nonane
ASER214DD9: nonane
AGLY218-PHE219DD9: nonane
ALEU221-ILE222DD9: nonane
AARG225DD9: nonane

MYS_5b6y_A_60610PENTADECANE binding site
ChainResidueligand
AALA184MYS: PENTADECANE
AVAL187-VAL188MYS: PENTADECANE
AILE191MYS: PENTADECANE
AILE198-PRO200MYS: PENTADECANE
AILE203MYS: PENTADECANE
ALEU207MYS: PENTADECANE
ALEU211MYS: PENTADECANE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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