EMDB < Search results

EMBL

was set up in 1974 as Europe’s flagship laboratory for the life sciences – an intergovernmental organisation with more than 80 independent research groups covering the spectrum of molecular biology:

Research:

perform basic research in molecular biology

Services:

offer vital services to scientists in the member states

Training

scientists, students and visitors at all levels

Transfer

and development of technology

Develop

new instruments and methods

Integrating

life science research in Europe

More about EMBL

Six sites

represent EMBL in Europe.

Barcelona

Tissue biology and disease modelling

Grenoble

Structural biology

Hamburg

Structural biology

Heidelberg

Main laboratory

Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

Edit your search query here and hit Return to execute it:

author:"He H" AND author_name:"Xin Y"

Sort by: Download

Showing 1 - 7 of 7. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [7]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

EMD-36984

Download Map 3D View

Cryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 3.3 angstrom

Release date: March 6, 2024
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8k9e

Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X

Plant Cell (2024) 36 pp. 4212-4233 [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]

Sample:

Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Heme c (618 Da, Ligand)
1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
[(2s)-2-octadecanoyloxypropyl] octadecanoate (609 Da, Ligand)
Fe3-s4 cluster (295 Da, Ligand)
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Iron/sulfur cluster (351 Da, Ligand)
Uncharacterized protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))

[Show more]

EMD-36985

Download Map 3D View

Cryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 2.9 angstrom

Release date: March 6, 2024
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8k9f

Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X

Plant Cell (2024) 36 pp. 4212-4233 [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]

Sample:

Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Hypothetical protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Heme c (618 Da, Ligand)
Magnesium ion (24 Da, Ligand)
1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Fe3-s4 cluster (295 Da, Ligand)
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Iron/sulfur cluster (351 Da, Ligand)

[Show more]

EMD-38012

Download Map 3D View

Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus

Release date: March 6, 2024
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8x2j

Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X

Plant Cell (2024) 36 pp. 4212-4233 [ DOI: doi:10.1093/plcell/koae029 Pubmed: 38299372 ]

Sample:

Polysulphide reductase nrfd (55 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate (663 Da, Ligand)
Alternative complex iii (Complex from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase membrane protein (19 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Fe-s-cluster-containing hydrogenase components 1-like protein (113 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 (45 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Heme c (618 Da, Ligand)
1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate (765 Da, Ligand)
Unknown (4 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Fe3-s4 cluster (295 Da, Ligand)
2-heptyl-4-hydroxy quinoline n-oxide (259 Da, Ligand)
[(2~{r})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate (663 Da, Ligand)
Cytochrome c7-like domain-containing protein (25 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Cytochrome c domain-containing protein (23 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Iron/sulfur cluster (351 Da, Ligand)
Uncharacterized protein (12 kDa, Protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))

[Show more]

EMD-34838

Download Map 3D View

Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 10,000 lux

Release date: Sept. 20, 2023
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8hju
Q-score: 0.603

Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X

eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]

Sample:

Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
The native rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Bacteriochlorophyll a (911 Da, Ligand)
Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Protoporphyrin ix containing fe (616 Da, Ligand)
Diacyl glycerol (625 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Beta,psi-caroten-4-one (550 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)

[Show more]

EMD-34839

Download Map 3D View

Cryo-EM structure of carotenoid-depleted RC-LH complex from Roseiflexus castenholzii at 10,000 lux

Release date: Sept. 20, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hjv
Q-score: 0.478

Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X

eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]

Sample:

Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Bacteriochlorophyll a (911 Da, Ligand)
Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
The carotenoid-depleted rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
Protoporphyrin ix containing fe (616 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Beta,psi-caroten-4-one (550 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)

[Show more]

EMD-35988

Download Map 3D View

Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux

Release date: Sept. 20, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j5o
Q-score: 0.606

Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X

eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]

Sample:

Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
The native rc-lh complex at 100lux (Complex from Roseiflexus castenholzii DSM 13941)
Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Bacteriochlorophyll a (911 Da, Ligand)
Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Protoporphyrin ix containing fe (616 Da, Ligand)
Bacteriopheophytin a (889 Da, Ligand)
Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
Beta,psi-caroten-4-one (550 Da, Ligand)
Fe (iii) ion (55 Da, Ligand)
Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)

[Show more]

EMD-35989

Download Map 3D View

Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 2,000lux

Release date: Sept. 20, 2023
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8j5p
Q-score: 0.562

Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X

eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]

Sample:

Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Bacteriochlorophyll a (911 Da, Ligand)
Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Protoporphyrin ix containing fe (616 Da, Ligand)
Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
Bacteriopheophytin b (887 Da, Ligand)
2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
Beta,psi-caroten-4-one (550 Da, Ligand)
The native rc-lh complex at 2,000lux (Complex from Roseiflexus castenholzii DSM 13941)
Fe (iii) ion (55 Da, Ligand)
Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)

[Show more]

Sort by: Download

Showing 1 - 7 of 7. Page 1 of 1

Display: Statistics

Download

Select database:

EMDB [7]

Format:

Select the script type:

Shell (Unix-based) Batch (Windows-based)

Preview first 10

Field: