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- PDB-1fbb: CRYSTAL STRUCTURE OF NATIVE CONFORMATION OF BACTERIORHODOPSIN -

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Basic information

Entry
Database: PDB / ID: 1fbb
TitleCRYSTAL STRUCTURE OF NATIVE CONFORMATION OF BACTERIORHODOPSIN
ComponentsBACTERIORHODOPSIN
KeywordsPROTON TRANSPORT / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / TWO-DIMENSIONAL CRYSTAL ELECTRON DIFFRACTION / SINGLE CRYSTAL
Function / homology
Function and homology information


photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.2 Å
AuthorsSubramaniam, S. / Henderson, R.
CitationJournal: Nature / Year: 2000
Title: Molecular mechanism of vectorial proton translocation by bacteriorhodopsin.
Authors: S Subramaniam / R Henderson /
Abstract: Bacteriorhodopsin, a membrane protein with a relative molecular mass of 27,000, is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium ...Bacteriorhodopsin, a membrane protein with a relative molecular mass of 27,000, is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum. The chromophore retinal is covalently attached to the protein via a protonated Schiff base. Upon illumination, retinal is isomerized. The Schiff base then releases a proton to the extracellular medium, and is subsequently reprotonated from the cytoplasm. An atomic model for bacteriorhodopsin was first determined by Henderson et al, and has been confirmed and extended by work in a number of laboratories in the last few years. Here we present an atomic model for structural changes involved in the vectorial, light-driven transport of protons by bacteriorhodopsin. A 'switch' mechanism ensures the vectorial nature of pumping. First, retinal unbends, triggered by loss of the Schiff base proton, and second, a protein conformational change occurs. This conformational change, which we have determined by electron crystallography at atomic (3.2 A in-plane and 3.6 A vertical) resolution, is largely localized to helices F and G, and provides an 'opening' of the protein to protons on the cytoplasmic side of the membrane.
History
DepositionJul 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2018Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Data processing / Experimental preparation / Refinement description
Category: em_3d_reconstruction / em_image_scans ...em_3d_reconstruction / em_image_scans / em_single_particle_entity / exptl_crystal_grow / software
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Assembly

Deposited unit
A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0992
Polymers26,8141
Non-polymers2841
Water0
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2976
Polymers80,4433
Non-polymers8533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6580 Å2
ΔGint-53 kcal/mol
Surface area27070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.45, 62.45, 100.9
Angle α, β, γ (deg.)90, 90, 120
Int Tables number143
Space group name H-MP3
DetailsTrimer is present in vivo The crystals contain trimers related by crystal symmetry P3

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Components

#1: Protein BACTERIORHODOPSIN /


Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: P02945
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 167
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Bacteriorhodopsin / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal growTemperature: 310 K / Method: naturally occurring in vivo / pH: 7
Details: crystal size is increased by fusion and annealing using detergents, pH 7, naturally occurring in vivo, temperature 37K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-23 mg/mlprotein11
20.5 %(w/v)beta-octylglucopyranoside11
34 %(w/v)benzamidine11
41.75 Msodium phosphate11
51.8-2.3 Mammonium sulfate1reservoir

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Data collection

EM imaging

Specimen-ID: 1

IDAccelerating voltage (kV)DetailsIllumination modeModelModeTemperature (max) (K)CryogenNominal magnification (X)Electron source
112060 degree tilted specimensFLOOD BEAMFEI/PHILIPS EM420DIFFRACTION153
21000, 20, 45 degree + random degree tiltsFLOOD BEAMSIEMENS SULEIKABRIGHT FIELDBright-field microscopy5HELIUM66000
3100, 20, 45 degree + random degree tiltsSPOT SCANJEOL 100BBRIGHT FIELDBright-field microscopy158NITROGEN55000FIELD EMISSION GUN
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of real imagesNum. of diffraction images
221220GENERIC FILM52
3315GENERIC FILM20
11GENERIC FILM150
DiffractionMean temperature: 93 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: OTHER / Wavelength: 0.033
DetectorType: OTHER / Detector: FILM / Date: Jan 1, 1986
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.033 Å / Relative weight: 1
ReflectionResolution: 3.2→200 Å / Num. all: 7297 / Num. obs: 4749 / % possible obs: 65.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.173

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Processing

SoftwareName: CNS / Version: 0.9 / Classification: refinement
RefinementResolution: 3.2→200 Å / Stereochemistry target values: Engh & Huber
Details: For the tilt angles used, the maximal possible theoretical completeness of the data set is ~87%. The completeness of our data is close to this limit up to 3.5 Angstroms. The completeness ...Details: For the tilt angles used, the maximal possible theoretical completeness of the data set is ~87%. The completeness of our data is close to this limit up to 3.5 Angstroms. The completeness drops to 65.1% when all of the data to 3.2 Angstroms is included.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 514 -RANDOM
Rwork0.239 ---
all-7297 --
obs-4749 65.1 %-
Refinement stepCycle: LAST / Resolution: 3.2→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 20 0 1753
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYc_bond_d0.009
ELECTRON CRYSTALLOGRAPHYc_angle_deg1.4

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