[English] 日本語
Yorodumi
- PDB-4v9g: RC-LH1-PufX dimer complex from Rhodobacter sphaeroides -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v9g
TitleRC-LH1-PufX dimer complex from Rhodobacter sphaeroides
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Intrinsic membrane protein PufX
KeywordsPHOTOSYNTHESIS / antenna complex LH1 / Reaction Centre / chromophores / Photosynthetic Complexes / Photosynthetic Light Capture and electron transfer / Photosynthetic Chromophores / membrane spherical vesicles / PufX / quinol / quinone
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PHOSPHATE ION / SPHEROIDENE / UBIQUINONE-10 / Light-harvesting protein B-875 alpha chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PHOSPHATE ION / SPHEROIDENE / UBIQUINONE-10 / Light-harvesting protein B-875 alpha chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Intrinsic membrane protein PufX / Light-harvesting protein B-875 beta chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.78 Å
AuthorsQian, P. / Papiz, M.Z. / Jackson, P.J. / Brindley, A.A. / Ng, I.W. / Olsen, J.D. / Dickman, M.J. / Bullough, P.A. / Hunter, C.N.
CitationJournal: Biochemistry / Year: 2013
Title: Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX.
Authors: Qian, P. / Papiz, M.Z. / Jackson, P.J. / Brindley, A.A. / Ng, I.W. / Olsen, J.D. / Dickman, M.J. / Bullough, P.A. / Hunter, C.N.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4JC9, 4JCB
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A5: Light-harvesting protein B-875 alpha chain
AT: Light-harvesting protein B-875 alpha chain
AV: Light-harvesting protein B-875 alpha chain
AX: Light-harvesting protein B-875 alpha chain
A3: Light-harvesting protein B-875 alpha chain
A7: Light-harvesting protein B-875 alpha chain
AD: Light-harvesting protein B-875 alpha chain
AF: Light-harvesting protein B-875 alpha chain
A1: Light-harvesting protein B-875 alpha chain
AJ: Light-harvesting protein B-875 alpha chain
A2: Light-harvesting protein B-875 alpha chain
AN: Light-harvesting protein B-875 alpha chain
AP: Light-harvesting protein B-875 alpha chain
AZ: Light-harvesting protein B-875 alpha chain
AB: Intrinsic membrane protein PufX
AS: Light-harvesting protein B-875 beta chain
A9: Light-harvesting protein B-875 beta chain
AO: Light-harvesting protein B-875 beta chain
AQ: Light-harvesting protein B-875 beta chain
A6: Light-harvesting protein B-875 beta chain
AU: Light-harvesting protein B-875 beta chain
AW: Light-harvesting protein B-875 beta chain
AY: Light-harvesting protein B-875 beta chain
A4: Light-harvesting protein B-875 beta chain
A8: Light-harvesting protein B-875 beta chain
AE: Light-harvesting protein B-875 beta chain
AG: Light-harvesting protein B-875 beta chain
AI: Light-harvesting protein B-875 beta chain
AK: Light-harvesting protein B-875 beta chain
AH: Reaction center protein H chain
AL: Reaction center protein L chain
AM: Reaction center protein M chain
B5: Light-harvesting protein B-875 alpha chain
BT: Light-harvesting protein B-875 alpha chain
BV: Light-harvesting protein B-875 alpha chain
BX: Light-harvesting protein B-875 alpha chain
B3: Light-harvesting protein B-875 alpha chain
B7: Light-harvesting protein B-875 alpha chain
BD: Light-harvesting protein B-875 alpha chain
BF: Light-harvesting protein B-875 alpha chain
B1: Light-harvesting protein B-875 alpha chain
BJ: Light-harvesting protein B-875 alpha chain
B2: Light-harvesting protein B-875 alpha chain
BN: Light-harvesting protein B-875 alpha chain
BP: Light-harvesting protein B-875 alpha chain
BZ: Light-harvesting protein B-875 alpha chain
BB: Intrinsic membrane protein PufX
BS: Light-harvesting protein B-875 beta chain
B9: Light-harvesting protein B-875 beta chain
BO: Light-harvesting protein B-875 beta chain
BQ: Light-harvesting protein B-875 beta chain
B6: Light-harvesting protein B-875 beta chain
BU: Light-harvesting protein B-875 beta chain
BW: Light-harvesting protein B-875 beta chain
BY: Light-harvesting protein B-875 beta chain
B4: Light-harvesting protein B-875 beta chain
B8: Light-harvesting protein B-875 beta chain
BE: Light-harvesting protein B-875 beta chain
BG: Light-harvesting protein B-875 beta chain
BI: Light-harvesting protein B-875 beta chain
BK: Light-harvesting protein B-875 beta chain
BH: Reaction center protein H chain
BL: Reaction center protein L chain
BM: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)619,063140
Polymers553,70964
Non-polymers65,35476
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.077, 415.075, 129.818
Angle α, β, γ (deg.)90.00, 105.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Light-harvesting protein B-875 ... , 2 types, 56 molecules A5ATAVAXA3A7ADAFA1AJA2ANAPAZB5BTBVBXB3B7BDBFB1BJB2BNBPBZASA9...

#1: Protein ...
Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6816.169 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0X9
#3: Protein/peptide ...
Light-harvesting protein B-875 beta chain / Antenna pigment protein beta chain / LH-3A


Mass: 5592.361 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J1A3

-
Protein , 1 types, 2 molecules ABBB

#2: Protein Intrinsic membrane protein PufX


Mass: 9061.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P13402

-
Reaction center protein ... , 3 types, 6 molecules AHBHALBLAMBM

#4: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y7
#5: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31477.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y8
#6: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34529.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Photosynthetic membranes / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y9

-
Non-polymers , 6 types, 76 molecules

#7: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#9: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4
#10: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#12: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O

-
Details

Sequence detailsTHE ISOLATED SAMPLE DOES NOT HAVE THE SAME NUMBER OF AMINO ACID RESIDUES CODED IN DNA FOR PROTEIN ...THE ISOLATED SAMPLE DOES NOT HAVE THE SAME NUMBER OF AMINO ACID RESIDUES CODED IN DNA FOR PROTEIN PUFX (CHAIN B). PUFX HAS 82 AMINO ACID RESIDUES BASED ON ITS DNA SEQUENCE. IT HAS BEEN SHOWN TO BE POSTRANSLATIONALLY MODIFIED AND THE LAST 12 RESIDUES ARE ABSENT (RATCLIFFE ET AL (2011), BIOCHIMICA ET BIOPHYSICA ACTA,1807,95-107).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 292 K / pH: 10.5
Details: The core dimer complex was concentrated to an optical density of ~100 at 875 nm and washed in (0.42%) n-nonyl- -D maltopyranoside to exchange the purification detergent, n-dodecyl- -D- ...Details: The core dimer complex was concentrated to an optical density of ~100 at 875 nm and washed in (0.42%) n-nonyl- -D maltopyranoside to exchange the purification detergent, n-dodecyl- -D-maltopyranoside. Crystals grew in 14.00% PEG400, 0.10 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS) pH 10.5, and 1.0% spermidine., VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.912
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Details: SI(111) SINGLE CRYSTAL MONOCHROMATOR AND VERTICALLY FOCUSSING SI CRYSTAL MIRROR
RadiationMonochromator: SI(111) SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.883
11-H, -K, H+L20.117
ReflectionResolution: 7.78→20.39 Å / Num. obs: 6831 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.6
Reflection shellResolution: 7.78→8.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1 / % possible all: 80

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OBTAINED BY FITTING 2D CRYO- ELECTRONMYCROSCOPY IMAGES

Resolution: 7.78→20.39 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.893 / SU B: 300.261 / SU ML: 2.374 / Cross valid method: THROUGHOUT / ESU R Free: 1.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25767 311 4.9 %RANDOM
Rwork0.22793 ---
obs0.22939 5997 73.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 250.037 Å2
Baniso -1Baniso -2Baniso -3
1--138.15 Å2-0 Å2-153.97 Å2
2--76.04 Å20 Å2
3---62.11 Å2
Refinement stepCycle: LAST / Resolution: 7.78→20.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17267 0 1826 0 19093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0239880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.632.05755546
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.76254240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25722.5571502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.091155284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.22415152
X-RAY DIFFRACTIONr_chiral_restr0.0830.25720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02131474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.78→7.95 Å / Total num. of bins used: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more