2024-11-13
REL
PDBe
PDBe
PDBe
2021-06-23
2021-09-22
2021-09-22
2024-11-13
Biotechnology and Biological Sciences Research Council (BBSRC)
BB/M000265/1
United Kingdom
European Research Council (ERC)
Synergy Award 854126
European Union
Wellcome Trust
209407/Z/17/Z
United Kingdom
Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Qian P
Croll TI
photosynthesis, light-harvesting complex, reaction centre, purple bacteria, membrane protein, STRUCTURAL PROTEIN
Qian P
Croll TI
Swainsbury DJK
Castro-Hartmann P
Moriarty NW
Sader K
Hunter CN
Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 angstrom.
Biochem.J.
UK
478
3253
3263
2021
34402504
doi:10.1042/BCJ20210511
1470-8728
0043
BIJOAK
7oy8
FULLOVERLAP
RC-LH1 from rhodospirillum rubrum
RC-LH1 from rhodospirillum rubrum
0
1
2
3
4
5
6
A reaction centre light harvesting core complex from purple bacterium ops. rubrum.
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
S1
297.7
Light-harvesting protein B-870 beta chain
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.006083941
16
LEVO
EVKQESLSGITEGEAKEFHKIFTSSILVFFGVAAFAHLLVWIWRPWVPGPNGYS
Q2RQ23
Antenna complex, alpha/beta subunit
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.005920986
15
LEVO
(FME)WRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGASTKPVQ
Q2RQ24
Photosynthetic reaction center, H-chain
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.027976192999999996
1
LEVO
MNKGDITGYMDVAQVVLYAFWIFFAGLIIYLRREDRREGYPLEDAISGKINSLQGLGSVFSIARPKIFKLKTGATYAAPN
FKRDAVAIKATRTAPTAGAPFEPTGNPMTDAVGPAAYALRDELPDLTLGGQPAIVPLRVAPTFSVAAEDTDPRGLPVVDR
KGAVAGKVTDLWIDRASIAIRYLEVELAATPGRKVLLPFAATRINAKTKSKTVTVQSILARHFANVPTIAKTDSITRREE
DKVMAYYSSGYLYSDRV
Q2RWS4
Photosynthetic reaction center L subunit
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.030660688
1
LEVO
MALLSFERKYRVRGGTLIGGDLFDFWVGPFYVGFFGVTTLLFTVLGTALIVWGAALGPSWTFWQISINPPDVSYGLAMAP
MAKGGLWQIITFSAIGAFVSWALREVEICRKLGIGYHIPFAFGFAILAYVSLVVIRPVMMGAWGYGFPYGFMTHLDWVSN
TGYQYANFHYNPAHMLGITLFFTTCLALALHGSLILSAANPGKGEVVKGPEHENTYFQDTIGYSVGTLGIHRVGLILALS
AVVWSIICMILSGPIYTGSWPDWWLWWQKLPFWNHG
Q2RQ25
Reaction center protein M chain
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.034234547
1
LEVO
MSEYQNILTGVQVRTAPHSAPIAKGIFPRLGKPGFSYWLGKIGDAQIGPIYLGTTGVLSLVFGFFAIEIIGFNLLASVNW
SPMEFGRQFFWLGLEPPAAEYGLGFAPLAEGGWWQIAGFFLTTSILLWWVRMYRRARALKMGTHTAWAFASAIFLFLSLG
FIRPLLMGNFSESVPFGIFPHLEWTNSFSLNYGNFFYNPFHMLSIAFLYGSALLFAMHGATILAVSRLGGDREVEQITDR
GTAAERAALFWRWTMGFNATMESIHRWAWWFAVLCTFTGAIGILLTGTVVDNWFEWGVKHGLAPAP
Q2RQ26
Antenna complex, alpha/beta subunit
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
0.007112404
1
LEVO
MWRIWQLFDPRQALVGLATFLFVLALLIHFILLSTERFNWLEGASTKPVQTSMVMPSSDLAV
Q2RQ24
Trans-Geranyl BACTERIOCHLOROPHYLL A
0.0009014249999999999
37
07D
SPIRILLOXANTHIN
0.0005969249999999999
17
CRT
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
0.0007490069999999999
2
PGW
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
0.001241633
2
CD4
BACTERIOPHEOPHYTIN A
0.000889215
2
BPH
2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione
0.0008442999999999999
1
RQ0
UBIQUINONE-10
0.0008633429999999999
3
U10
FE (III) ION
5.5845e-05
1
FE
CHLORIDE ION
3.5453e-05
1
CL
PHOSPHATE ION
9.4971e-05
1
PO4
DODECYL-BETA-D-MALTOSIDE
0.000510615
1
LMT
water
1.8015e-05
372
HOH
singleParticle
particle
4.0
8.0
20.0
C8H18N2O4S
HEPES
20 mM HEPES, 0.03% beta DDM, pH 8.0
Quantifoil
COPPER
400
GLOW DISCHARGE
AIR
ETHANE
100
277
FEI VITROBOT MARK IV
Quantifiol R1.2/1.3 grid, glow discharged.
bloting time: 2.5, bloting force 3, waiting time 0.
The protein were solubilised using detergent beta DDM, and purified by the use of ion exchange column and size exclusion column. Monodisperse sample was used for cry-EM preparation.
FEI TITAN KRIOS
FLOOD BEAM
BRIGHT FIELD
FIELD EMISSION GUN
300
2.7
120000.0
FEI TITAN KRIOS AUTOGRID HOLDER
NITROGEN
FEI FALCON IV (4k x 4k)
1
9024
12.12
45.0
total dose of 45 was fractionated to 42 frames within 12.12 second.
1
Images were motion corrected and CTF corrected.
1519688
Selected 2D classes were used to build up an initial model using EMAN2.
1
C1
BACK PROJECTION
2.5
FSC 0.143 CUT-OFF
RELION
3.1
519005
COMMON LINE
EMAN2
COMMON LINE
RELION
3.1
4
RELION
3.1
A best 3D class was selected.
1LGH
PDB
experimental model
3I4D
PDB
experimental model
FLEXIBLE FIT
REAL