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- PDB-2brd: CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE -

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Entry
Database: PDB / ID: 2brd
TitleCRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE
ComponentsBACTERIORHODOPSIN
KeywordsPHOTORECEPTOR / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / TWO-DIMENSIONAL CRYSTAL
Function / homology
Function and homology information


light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / monoatomic ion channel activity / proton transmembrane transport / 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
Chem-DPG / RETINAL / Bacteriorhodopsin
Similarity search - Component
Biological speciesHalobacterium salinarum (Halophile)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.5 Å
AuthorsHenderson, R. / Grigorieff, N.
Citation
Journal: J Mol Biol / Year: 1996
Title: Electron-crystallographic refinement of the structure of bacteriorhodopsin.
Authors: N Grigorieff / T A Ceska / K H Downing / J M Baldwin / R Henderson /
Abstract: Using electron diffraction data corrected for diffuse scattering together with additional phase information from 30 new images of tilted specimens, an improved experimental density map has been ...Using electron diffraction data corrected for diffuse scattering together with additional phase information from 30 new images of tilted specimens, an improved experimental density map has been calculated for bacteriorhodopsin. The atomic model has then been rebuilt into this new map with particular attention to the surface loops. All the residues from 7 to 227 as well as ten lipid molecules are now included, although a few amino acid residues in three of the six surface loops, about half of the lipid hydrophobic chains and all of the lipid head groups are disordered. The model has then been refined against the experimental diffraction amplitudes to an R-factor of 28% at 3.5 angstrom resolution with strict geometry (0.005 angstrom) bond length deviation) using the improvement of the "free" phase residual between calculated and experimental phases from images as an objective criterion of accuracy. For the refinement some new programs were developed to restrain the number of parameters, to be compatible with the limited resolution of our data. In the final refined model of the protein (2BRD), compared with earlier co-ordinates (1BRD), helix D has been moved towards the cytoplasm by almost 4 angstrom, and the overall accuracy of the co-ordinates of residues in the other six helices has been improved. As a result the positions of nearly all the important residues in bacteriorhodopsin are now well determined. In particular, the buried, protonated Asp115 is 7 angstrom from, and so not in contact with, the retinal and Met118 forms a cap on the pocket occupied by the beta-ionone ring. No clear density exists for the side-chain of Arg82, which forms a central part of the extracellular half-channel. The only arginine side-chain built into good density is that of Arg134 at the extracellular end of helix E, the others being disordered near one of the two surfaces. The interpretation of the end of helix F on the extracellular surface is now clearer; an extra loose helical turn has been built bringing the side-chain of Glu194 close to Arg134 to form a probable salt bridge. The model provides an improved framework for understanding the mechanism of the light-driven proton pumping. A number of cavities that could contain water molecules were found by searching the refined model, most of them above or below the Schiff base in the half-channels leading to the two surfaces. The ordered and disordered regions of the structure are described by the temperature factor distribution.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Analysis of High-Resolution Electron Diffraction Patterns from Purple Membrane Labelled with Heavy-Atoms
Authors: Ceska, T.A. / Henderson, R.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Model for the Structure of Bacteriorhodopsin Based on High-Resolution Electron Cryo-Microscopy
Authors: Henderson, R. / Baldwin, J.M. / Ceska, T.A. / Zemlin, F. / Beckmann, E. / Downing, K.H.
#3: Journal: Nature / Year: 1975
Title: Three-Dimensional Model of Purple Membrane Obtained by Electron Microscopy
Authors: Henderson, R. / Unwin, P.N.
History
DepositionDec 27, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 30, 2012Group: Experimental preparation
Revision 2.0Jun 5, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation / em_image_scans / em_single_particle_entity / entity_poly / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation.pdbx_scattering_type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Assembly

Deposited unit
A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,95412
Polymers26,7971
Non-polymers9,15611
Water00
1
A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules

A: BACTERIORHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,86136
Polymers80,3923
Non-polymers27,46933
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 area34840 Å2
ΔGint-277 kcal/mol
Surface area35800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.450, 62.450, 100.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein BACTERIORHODOPSIN


Mass: 26797.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (Halophile) / Strain: R1 / References: UniProt: P02945
#2: Chemical
ChemComp-DPG / PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER / DPHPG


Mass: 887.195 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C46H96O11P2 / Comment: phospholipid*YM
#3: Chemical ChemComp-RET / RETINAL


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: BACTERIORHODOPSIN CRYSTAL / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal grow
*PLUS
Method: other / Details: electron-crystallographic method

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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 FIELD5HELIUM66000
3100, 20, 45 degree + random degree tiltsSPOT SCANJEOL 100BBRIGHT FIELD158NITROGEN55000FIELD 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
Diffraction sourceWavelength: 0.033
DetectorDetector: FILM / Date: Jan 1, 1986
RadiationMonochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.033 Å / Relative weight: 1
ReflectionResolution: 2.8→54 Å / Num. obs: 6750 / % possible obs: 62.3 % / Observed criterion σ(I): 0 / Redundancy: 18 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
PROLSQrefinement
PICKYCORdata reduction
ANMRC ELECTRON DIFFRACTION PROGRAMdata reduction
3D reconstructionSymmetry type: 2D CRYSTAL
RefinementResolution: 3.5→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.28 --
obs-4743 85.4 %
Displacement parametersBiso mean: 114 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 610 0 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
ELECTRON CRYSTALLOGRAPHYp_bond_d0.0050.02
ELECTRON CRYSTALLOGRAPHYp_angle_d0.020.04
ELECTRON CRYSTALLOGRAPHYp_angle_deg
ELECTRON CRYSTALLOGRAPHYp_planar_d0.0220.05
ELECTRON CRYSTALLOGRAPHYp_hb_or_metal_coord
ELECTRON CRYSTALLOGRAPHYp_mcbond_it
ELECTRON CRYSTALLOGRAPHYp_mcangle_it
ELECTRON CRYSTALLOGRAPHYp_scbond_it
ELECTRON CRYSTALLOGRAPHYp_scangle_it
ELECTRON CRYSTALLOGRAPHYp_plane_restr0.0050.02
ELECTRON CRYSTALLOGRAPHYp_chiral_restr0.0860.15
ELECTRON CRYSTALLOGRAPHYp_singtor_nbd0.1850.3
ELECTRON CRYSTALLOGRAPHYp_multtor_nbd0.2420.3
ELECTRON CRYSTALLOGRAPHYp_xhyhbond_nbd
ELECTRON CRYSTALLOGRAPHYp_xyhbond_nbd0.1270.3
ELECTRON CRYSTALLOGRAPHYp_planar_tor0.865
ELECTRON CRYSTALLOGRAPHYp_staggered_tor20.415
ELECTRON CRYSTALLOGRAPHYp_orthonormal_tor
ELECTRON CRYSTALLOGRAPHYp_transverse_tor36.120
ELECTRON CRYSTALLOGRAPHYp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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