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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yao, D."

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Search Summary

This query matches 63 Structures.

Refinements

Structure Determination Methodology

experimental (63)

Scientific Name of Source Organism

	Homo sapiens (46)
	Gallus gallus (3)
	Hyphomonas neptunium ATCC 15444 (3)
	Shigella flexneri (3)
	Tequatrovirus T4 (3)
	Bacteroides thetaiotaomicron VPI-5482 (2)
	Phytophthora infestans T30-4 (2)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (2)
	synthetic construct (2)
	Escherichia coli (1)

More...

Taxonomy

	Eukaryota (53)
	Bacteria (11)
	Duplodnaviria (3)
	other sequences (2)

Experimental Method

	ELECTRON MICROSCOPY (40)
	X-RAY DIFFRACTION (23)

Polymer Entity Type

Protein (63)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (5)
	2.5 - 3.0 (12)
	3.0 - 3.5 (21)
	3.5 - 4.0 (19)
	4.0 - 4.5 (1)
	> 4.5 (2)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (5)
	2015 - 2019 (8)
	2020 - 2024 (45)
	2025 - 2029 (4)

Enzyme Classification Name

	Transferases (10)
	Oxidoreductases (11)
	Hydrolases (6)
	Isomerases (5)

Membrane Protein Annotation

	PDBTM (34)
	MemProtMD (20)
	mpstruc (20)
	OPM (12)

Symmetry Type

	Asymmetric (32)
	Cyclic (31)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	Small proteins (1)

AllSelected

1 to 25 of 63 Structures

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2EXX \| pdb_00002exx	Download File View File

Crystal structure of HSCARG from Homo sapiens in complex with NADP

Dai, X., Chen, Q., Yao, D., Liang, Y., Dong, Y., Gu, X., Zheng, X., Luo, M.

(2007) Proc Natl Acad Sci U S A 104: 8809-8814

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	HSCARG protein (protein)
Unique Ligands	GOL, NAP

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4E29 \| pdb_00004e29	Download File View File

Periplasmic domain of the chimeric WzzB chain length regulator protein

Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

(2012) J Biological Chem 287: 15696-15705

Released	2012-03-28
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Shigella flexneri
Macromolecule	Chimeric WzzB chain length determinant protein (protein)

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4E2C \| pdb_00004e2c	Download File View File

Crystal Structure of the periplasmic domain of the chimeric LPS O-antigen chain length regulator protein

Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

(2012) J Biological Chem 287: 15696-15705

Released	2012-03-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Shigella flexneri
Macromolecule	chimeric WzzB Chain length determinant protein (protein)

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4E2H \| pdb_00004e2h	Download File View File

Crystal structure of the periplasmic domain of Shigella flexneri WzzB

Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

(2012) J Biological Chem 287: 15696-15705

Released	2012-03-28
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Shigella flexneri
Macromolecule	Chain length determinant protein (protein)

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4E2L \| pdb_00004e2l	Download File View File

Crystal Structure of the periplasmic domain of mutant FepE LPS O-antigen chain length regulator protein

Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

(2012) J Biological Chem 287: 15696-15705

Released	2012-03-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Escherichia coli O157:H7
Macromolecule	Ferric enterobactin (Enterochelin) transport (protein)

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4MU6 \| pdb_00004mu6	Download File View File

Crystal Structure of the N-terminal domain of Effector Protein LegC3 from Legionella pneumophila

Yao, D., Cherney, M., Cygler, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 436-441

Released	2013-12-11
Method	X-RAY DIFFRACTION 2.082 Å
Organisms	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Macromolecule	Kinectin 1 (Kinesin receptor) (protein)

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5JMD \| pdb_00005jmd	Download File View File

Heparinase III-BT4657 gene product, Methylated Lysines

Ulaganathan, T.S., Shi, R., Yao, D., Garron, M.-L., Cherney, M., Cygler, M.

(2017) Glycobiology 27: 176-187

Released	2016-05-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	Heparinase III protein (protein)
Unique Ligands	MG

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5JMF \| pdb_00005jmf	Download File View File

Heparinase III-BT4657 gene product

Ulaganathan, T.S., Shi, R., Yao, D., Garron, M.-L., Cherney, M., Cygler, M.

(2017) Glycobiology 27: 176-187

Released	2016-05-25
Method	X-RAY DIFFRACTION 1.854 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	Heparinase III protein (protein)
Unique Ligands	GOL, MG, TRS

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6D26 \| pdb_00006d26	Download File View File

Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant

Wang, L., Yao, D., Deepak, K., Liu, H., Gong, W., Fan, H., Wei, Z., Zhang, C.

(2018) Mol Cell 72: 48-59.e4

Released	2018-10-03
Method	X-RAY DIFFRACTION 2.798 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Prostaglandin D2 receptor 2, Endolysin chimera (protein)
Unique Ligands	FSY, OLA, PGE, PGO, SIN, SO4

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6D27 \| pdb_00006d27	Download File View File

Crystal structure of the prostaglandin D2 receptor CRTH2 with CAY10471

Wang, L., Yao, D., Deepak, K., Liu, H., Gong, W., Fan, H., Wei, Z., Zhang, C.

(2018) Mol Cell 72: 48-59.e4

Released	2018-10-03
Method	X-RAY DIFFRACTION 2.738 Å
Organisms	Homo sapiens Tequatrovirus T4
Macromolecule	Prostaglandin D2 receptor 2, Endolysin chimera (protein)
Unique Ligands	FT4, MES, OLA, PEG, PGE, PGO, SO4

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6E8J \| pdb_00006e8j	Download File View File

Crystal Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster, in Inward-facing And Occupied Conformation

Zhou, F., Yao, D., Rao, B., Zhang, L., Cao, Y.

(2019) Sci Bull (Beijing) 64: 1310-1317

Released	2019-08-14
Method	X-RAY DIFFRACTION 3.091 Å
Organisms	Hyphomonas neptunium ATCC 15444
Macromolecule	Major facilitator family transporter (protein)

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6E9C \| pdb_00006e9c	Download File View File

Selenomethionine Derivative Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster

Zhou, F., Yao, D., Rao, B., Zhang, L., Cao, Y.

(2019) Sci Bull (Beijing) 64: 1310-1317

Released	2019-08-14
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Hyphomonas neptunium ATCC 15444
Macromolecule	Major facilitator family transporter (protein)

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6EBA \| pdb_00006eba	Download File View File

Crystal Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster, in Inward-facing And Unoccupied Conformation

Zhou, F., Yao, D., Rao, B., Zhang, L., Cao, Y.

(2019) Sci Bull (Beijing) 64: 1310-1317

Released	2019-08-21
Method	X-RAY DIFFRACTION 3.812 Å
Organisms	Hyphomonas neptunium ATCC 15444
Macromolecule	Major facilitator family transporter (protein)

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6KXW \| pdb_00006kxw	Download File View File

Crystal structure of human aquaporin AQP7 in bound to glycerol

Zhang, L., Yao, D., Zhou, F., Zhang, Q., Zhou, L., Cao, Y.

(2020) Sci Bull (Beijing) 66: 1550-1558

Released	2019-11-27
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Homo sapiens
Macromolecule	Aquaporin-7 (protein)
Unique Ligands	GOL

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7C96 \| pdb_00007c96	Download File View File

Avr1d:GmPUB13 U-box

Xing, W., Hu, Q., Zhou, J., Yao, D.

(2021) Proc Natl Acad Sci U S A 118:

Released	2021-03-17
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Glycine soja Phytophthora sojae strain P6497
Macromolecule	RING-type E3 ubiquitin transferase (protein) RxLR effector protein Avh6 (protein)

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7CZB \| pdb_00007czb	Download File View File

The cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1

Rao, B., Li, S., Yao, D., Wang, Q., Xia, Y., Jia, Y., Shen, Y., Cao, Y.

(2021) Sci Adv 7:

Released	2021-03-17
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens
Macromolecule	Derlin-1 (protein)

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7E40 \| pdb_00007e40	Download File View File

Mechanism of Phosphate Sensing and Signaling Revealed by Rice SPX1-PHR2 Complex Structure

Zhou, J., Hu, Q., Yao, D., Xing, W.

(2021) Nat Commun 12: 7040-7040

Released	2021-11-10
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Oryza sativa Japonica Group Tequatrovirus T4
Macromolecule	Protein PHOSPHATE STARVATION RESPONSE 2 (protein) SPX domain-containing protein 1,Endolysin (protein)
Unique Ligands	IHP

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7EWT \| pdb_00007ewt	Download File View File

The crystal structure of Lysophospholipid acyltransferase LPCAT3 (MOBAT5) in its monomeric and apo form

Zhang, Q., Yao, D., Rao, B., Li, S., Jian, L., Chen, Y., Hu, K., Xia, Y., Cao, Y.

(2021) Nat Commun 12: 6869-6869

Released	2021-12-01
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Gallus gallus
Macromolecule	Lysophospholipid acyltransferase 5 (protein)

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7EZC \| pdb_00007ezc	Download File View File

Adenosine A2a receptor mutant-I92N

Cui, M., Zhou, Q., Yao, D., Zhao, S., Song, G.

(2022) IUCrJ 9: 333-341

Released	2022-04-13
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a,Soluble cytochrome b562 (protein)
Unique Ligands	UKA

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7F3X \| pdb_00007f3x	Download File View File

Lysophospholipid acyltransferase LPCAT3 in complex with lysophosphatidylcholine

Zhang, Q., Yao, D., Rao, B., Li, S., Jian, L., Chen, Y., Hu, K., Xia, Y., Shen, Y., Cao, Y.

(2021) Nat Commun 12: 6869-6869

Released	2021-12-01
Method	ELECTRON MICROSCOPY 3.57 Å
Organisms	Gallus gallus
Macromolecule	LPCAT3 (protein)
Unique Ligands	LAP

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7F40 \| pdb_00007f40	Download File View File

Lysophospholipid acyltransferase LPCAT3 in a complex with Arachidonoyl-CoA

Zhang, Q., Yao, D., Rao, B., Li, S., Jian, L., Chen, Y., Hu, K., Xia, Y., Shen, Y., Cao, Y.

(2021) Nat Commun 12: 6869-6869

Released	2021-12-01
Method	ELECTRON MICROSCOPY 3.49 Å
Organisms	Gallus gallus
Macromolecule	LPCAT3 (protein)
Unique Ligands	3IX, PCW

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7XP9 \| pdb_00007xp9	Download File View File

Phytophthora infesfans RxLR effector AVRvnt1

Xing, W., Hu, Q., Zhou, J., Yao, D.

To be published

Released	2023-06-07
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Phytophthora infestans T30-4
Macromolecule	RxLR effector protein Avr-vnt11 (protein)

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7XPC \| pdb_00007xpc	Download File View File

Complex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1

Hu, Q., Zhou, J., Yao, D., Xing, W.

To be published

Released	2023-06-07
Method	X-RAY DIFFRACTION 3.31 Å
Organisms	Phytophthora infestans T30-4 Solanum lycopersicum
Macromolecule	D-glycerate-3-kinase (GLYK) (protein) RxLR effector protein Avr-vnt11 (protein)

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7Y4W \| pdb_00007y4w	Download File View File

The cryo-EM structure of human ERAD retro-translocation complex

Cao, Y., Rao, B., Wang, Q., Yao, D., Xia, Y., Li, W., Li, S., Shen, Y.

(2023) Sci Adv 9: eadi5656-eadi5656

Released	2023-10-18
Method	ELECTRON MICROSCOPY 3.67 Å
Organisms	Homo sapiens
Macromolecule	Derlin-1 (protein) Transitional endoplasmic reticulum ATPase (protein)
Unique Ligands	ADP

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7Y53 \| pdb_00007y53	Download File View File

The cryo-EM structure of human ERAD retro-translocation complex

Cao, Y., Rao, B., Wang, Q., Yao, D., Xia, Y., Li, W., Li, S., Shen, Y.

(2023) Sci Adv 9: eadi5656-eadi5656

Released	2023-10-18
Method	ELECTRON MICROSCOPY 3.61 Å
Organisms	Homo sapiens
Macromolecule	Derlin-1 (protein) Transitional endoplasmic reticulum ATPase (protein)
Unique Ligands	ADP

1 to 25 of 63 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2EXX | pdb_00002exx

4E29 | pdb_00004e29

4E2C | pdb_00004e2c

4E2H | pdb_00004e2h

4E2L | pdb_00004e2l

4MU6 | pdb_00004mu6

5JMD | pdb_00005jmd

5JMF | pdb_00005jmf

6D26 | pdb_00006d26

6D27 | pdb_00006d27

6E8J | pdb_00006e8j

6E9C | pdb_00006e9c

6EBA | pdb_00006eba

6KXW | pdb_00006kxw

7C96 | pdb_00007c96

7CZB | pdb_00007czb

7E40 | pdb_00007e40

7EWT | pdb_00007ewt

7EZC | pdb_00007ezc

7F3X | pdb_00007f3x

7F40 | pdb_00007f40

7XP9 | pdb_00007xp9

7XPC | pdb_00007xpc

7Y4W | pdb_00007y4w

7Y53 | pdb_00007y53