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- PDB-3am6: Crystal structure of the proton pumping rhodopsin AR2 from marine... -

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Basic information

Entry
Database: PDB / ID: 3am6
TitleCrystal structure of the proton pumping rhodopsin AR2 from marine alga Acetabularia acetabulum
Componentsrhodopsin-2
KeywordsTRANSPORT PROTEIN / seven trans-membrane
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane
Similarity search - Function
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
CHOLESTEROL / RETINAL / Rhodopsin-2
Similarity search - Component
Biological speciesAcetabularia acetabulum (mermaid's wine glass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWada, T. / Yokoyama, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga
Authors: Wada, T. / Shimono, K. / Kikukawa, T. / Hato, M. / Shinya, N. / Kim, S.Y. / Kimura-Someya, T. / Shirouzu, M. / Tamogami, J. / Miyauchi, S. / Jung, K.-H. / Kamo, N. / Yokoyama, S.
History
DepositionAug 16, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rhodopsin-2
B: rhodopsin-2
C: rhodopsin-2
D: rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,48416
Polymers102,2534
Non-polymers4,23112
Water00
1
A: rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6214
Polymers25,5631
Non-polymers1,0583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6214
Polymers25,5631
Non-polymers1,0583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6214
Polymers25,5631
Non-polymers1,0583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: rhodopsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6214
Polymers25,5631
Non-polymers1,0583
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-41 kcal/mol
Surface area39570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.120, 110.487, 129.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 7 - 225 / Label seq-ID: 7 - 225

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
rhodopsin-2 / AR2


Mass: 25563.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetabularia acetabulum (mermaid's wine glass)
Plasmid: pCR2.1-TOPO / Production host: cell-free synthesis (others) / References: UniProt: G1K3Q0*PLUS
#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H46O
Has protein modificationY
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEINS AT THE TIME OF PROCESSING. THE ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEINS AT THE TIME OF PROCESSING. THE SEQUENCE HAS BEEN DEPOSITED ON GENBANK WITH THE ACCESSION CODE, HM070408.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 293 K / Method: lipid mesophase / pH: 7.5
Details: 0.1M Tris-HCl (pH 7.5), 6% 2-methyl-2,4-pentanediol, 14% polyethylene glycol 400, lipid mesophase, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.192→50 Å / Num. obs: 18284 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.115 / Net I/σ(I): 8.7
Reflection shellResolution: 3.192→3.31 Å / Redundancy: 2.5 % / Rsym value: 0.251 / % possible all: 72.2

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Processing

Software
NameVersionClassification
BSSdata collection
MrBUMPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→36.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.837 / Rfactor Rfree error: 0.011 / SU B: 28.947 / SU ML: 0.505 / Data cutoff high absF: 53692.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.697 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.324 891 4.9 %RANDOM
Rwork0.29 ---
obs0.29 18250 89.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9644 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.54 Å20 Å20 Å2
2--17.34 Å20 Å2
3----10.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3.2→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 304 0 7328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 129 5.3 %
Rwork0.385 2313 -
obs--72.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2r+c+o.paramr+c+o.top

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