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- PDB-1brd: Model for the structure of Bacteriorhodopsin based on high-resolu... -

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Entry
Database: PDB / ID: 1brd
TitleModel for the structure of Bacteriorhodopsin based on high-resolution Electron Cryo-microscopy
ComponentsBACTERIORHODOPSIN PRECURSOR
KeywordsPHOTORECEPTOR
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: 3.5 Å
AuthorsHenderson, R. / Baldwin, J.M. / Ceska, T.A. / Zemlin, F. / Beckmann, E. / Downing, K.H.
Citation
Journal: J Mol Biol / Year: 1990
Title: Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.
Authors: R Henderson / J M Baldwin / T A Ceska / F Zemlin / E Beckmann / K H Downing /
Abstract: The light-driven proton pump bacteriorhodopsin occurs naturally as two-dimensional crystals. A three-dimensional density map of the structure, at near-atomic resolution, has been obtained by studying ...The light-driven proton pump bacteriorhodopsin occurs naturally as two-dimensional crystals. A three-dimensional density map of the structure, at near-atomic resolution, has been obtained by studying the crystals using electron cryo-microscopy to obtain electron diffraction patterns and high-resolution micrographs. New methods were developed for analysing micrographs from tilted specimens, incorporating methods previously developed for untilted specimens that enable large areas to be analysed and corrected for distortions. Data from 72 images, from both tilted and untilted specimens, were analysed to produce the phases of 2700 independent Fourier components of the structure. The amplitudes of these components were accurately measured from 150 diffraction patterns. Together, these data represent about half of the full three-dimensional transform to 3.5 A. The map of the structure has a resolution of 3.5 A in a direction parallel to the membrane plane but lower than this in the perpendicular direction. It shows many features in the density that are resolved from the main density of the seven alpha-helices. We interpret these features as the bulky aromatic side-chains of phenylalanine, tyrosine and tryptophan residues. There is also a very dense feature, which is the beta-ionone ring of the retinal chromophore. Using these bulky side-chains as guide points and taking account of bulges in the helices that indicate smaller side-chains such as leucine, a complete atomic model for bacteriorhodopsin between amino acid residues 8 and 225 has been built. There are 21 amino acid residues, contributed by all seven helices, surrounding the retinal and 26 residues, contributed by five helices, forming the proton pathway or channel. Ten of the amino acid residues in the middle of the proton channel are also part of the retinal binding site. The model also provides a useful basis for consideration of the mechanism of proton pumping and allows a consistent interpretation of a great deal of other experimental data. In particular, the structure suggests that pK changes in the Schiff base must act as the means by which light energy is converted into proton pumping pressure in the channel. Asp96 is on the pathway from the cytoplasm to the Schiff base and Asp85 is on the pathway from the Schiff base to the extracellular surface.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: Specific Labelling of the Protein and Lipid on the Extracellular Surface of Purple Membrane
Authors: Henderson, R. / Jubb, J.S. / Whytock, S.
#2: Journal: Nature / Year: 1975
Title: Three-Dimensional Model of Purple Membrane Obtained by Electron Microscopy
Authors: Henderson, R. / Unwin, P.N.T.
History
DepositionMay 23, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 26, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / diffrn_radiation / em_image_scans / entity_poly / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _diffrn_radiation.pdbx_scattering_type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Remark 650HELIX THE ENDS OF THE HELICES ARE UNCERTAIN BY AT LEAST ONE RESIDUE. IN ADDITION, PRO 50, PRO 91, ...HELIX THE ENDS OF THE HELICES ARE UNCERTAIN BY AT LEAST ONE RESIDUE. IN ADDITION, PRO 50, PRO 91, AND PRO 186 ARE IN THE MIDDLE OF HELICAL SEGMENTS BUT IN EACH CASE THE HELICES ARE BENT NEAR THE PROLINE RESIDUES.

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Structure visualization

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Assembly

Deposited unit
A: BACTERIORHODOPSIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0822
Polymers26,7971
Non-polymers2841
Water0
1
A: BACTERIORHODOPSIN PRECURSOR
hetero molecules

A: BACTERIORHODOPSIN PRECURSOR
hetero molecules

A: BACTERIORHODOPSIN PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2456
Polymers80,3923
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
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 62.450, 100.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Atom site foot note1: A TEMPERATURE FACTOR OF 99.0 DENOTES SIDE CHAINS WITH NO CLEAR DENSITY IN THE EXPERIMENTAL MAP OR WITH OTHER AMBIGUITY. A TEMPERATURE FACTOR OF 20.0 DENOTES GOOD SIDE CHAINS OR THE POLYPEPTIDE ...1: A TEMPERATURE FACTOR OF 99.0 DENOTES SIDE CHAINS WITH NO CLEAR DENSITY IN THE EXPERIMENTAL MAP OR WITH OTHER AMBIGUITY. A TEMPERATURE FACTOR OF 20.0 DENOTES GOOD SIDE CHAINS OR THE POLYPEPTIDE BACKBONE IN THE MAIN HELICAL SEGMENTS. SOME SIDE CHAINS OF INTERMEDIATE QUALITY HAVE TEMPERATURE FACTORS OF 40.0.

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Components

#1: Protein BACTERIORHODOPSIN PRECURSOR


Mass: 26797.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography
Crystal symmetry∠γ: 120 ° / C sampling length: 100 Å / A: 62.45 Å / B: 62.45 Å / C: 100 Å / Space group name H-M: P3

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Sample preparation

ComponentName: Bacteriorhodopsin from purple membrane / Type: COMPLEX
Buffer solutionpH: 5.2
Details: 0.1 mM potassium phosphate, 6 mM octyl glucoside, 0.2 mM trimethylammonium chloride
SpecimenConc.: 3 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: carbon aged several days to optimize hydrophobicity
Grid material: COPPER
EM embeddingDetails: 0.8% (w/v) glucose / Material: glucose

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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
RadiationScattering type: electron
Radiation wavelengthRelative weight: 1

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Processing

Crystal symmetry∠γ: 120 ° / C sampling length: 100 Å / A: 62.45 Å / B: 62.45 Å / C: 100 Å / Space group name H-M: P3
3D reconstructionResolution: 3.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
RefinementHighest resolution: 3.5 Å
Details: A TEMPERATURE FACTOR OF 99.0 DENOTES SIDE CHAINS WITH NO CLEAR DENSITY IN THE EXPERIMENTAL MAP OR WITH OTHER AMBIGUITY. A TEMPERATURE FACTOR OF 20.0 DENOTES GOOD SIDE CHAINS OR THE ...Details: A TEMPERATURE FACTOR OF 99.0 DENOTES SIDE CHAINS WITH NO CLEAR DENSITY IN THE EXPERIMENTAL MAP OR WITH OTHER AMBIGUITY. A TEMPERATURE FACTOR OF 20.0 DENOTES GOOD SIDE CHAINS OR THE POLYPEPTIDE BACKBONE IN THE MAIN HELICAL SEGMENTS. SOME SIDE CHAINS OF INTERMEDIATE QUALITY HAVE TEMPERATURE FACTORS OF 40.0. THIS STRUCTURE WAS REFINED WITH RESIDUE 111 SPECIFIED AS ILE. GENE SEQUENCING HAS SHOWN THAT THIS RESIDUE SHOULD BE LEU. THIS HAS BEEN CORRECTED IN THIS ENTRY BY RENAMING RESIDUE 111 AS LEU AND REMOVING THE SIDE CHAIN ATOMS BEYOND CB. THIS WILL BE CORRECTED IN FUTURE MORE ACCURATE COORDINATE SETS. THE DATA WAS COLLECTED ON 2-DIMENSIONAL CRYSTALS AND HENCE THE C-AXIS REPEAT DOES NOT CORRESPOND TO A REAL REPEAT, BUT INSTEAD REFERS TO THE SAMPLING THAT IS USED TO DESCRIBE THE CONTINUOUS TRANSFORM. THE C VALUE OF 100.0 IS THEREFORE THE VALUE WHICH SHOULD BE USED IN INTERPRETING THE MEANING OF THE L INDEX.
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 20 0 1363

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