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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Li, X.M."

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Homo sapiens (15)
	Monkeypox virus (5)
	synthetic construct (4)
	Enterobacter sp. Px6-4 (2)
	Mus musculus (2)
	Bos taurus (1)
	Brucella melitensis bv. 1 str. 16M (1)
	Porcine reproductive and respiratory syndrome virus (1)

Taxonomy

	Eukaryota (15)
	Varidnaviria (5)
	other sequences (4)
	Bacteria (3)
	Riboviria (1)

Experimental Method

	ELECTRON MICROSCOPY (13)
	X-RAY DIFFRACTION (9)
	ELECTRON CRYSTALLOGRAPHY (1)
	SOLUTION SCATTERING (1)

Polymer Entity Type

	Protein (24)
	DNA (5)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (4)
	2.5 - 3.0 (6)
	3.0 - 3.5 (10)
	3.5 - 4.0 (1)

Release Date

	2010 - 2014 (7)
	2015 - 2019 (2)
	2020 - 2024 (10)
	2025 - 2029 (5)

Enzyme Classification Name

	Hydrolases (11)
	Transferases (6)
	Lyases (2)

Membrane Protein Annotation

	PDBTM (8)
	OPM (6)
	mpstruc (3)
	MemProtMD (3)

Symmetry Type

	Asymmetric (18)
	Cyclic (8)

SCOP Classification

All beta proteins (2)

AllSelected

1 to 24 of 24 Structures

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3K2S \| pdb_00003k2s	Download File View File

Solution structure of double super helix model

Wu, Z., Gogonea, V., Lee, X., Wagner, M.A., Li, X.-M., Huang, Y., Undurti, A., May, R.P., Haertlein, M., Moulin, M., Gutsche, I., Zaccai, G., Didonato, J.A., Hazen, L.S.

(2009) J Biological Chem 284: 36605-36619

Released	2010-04-07
Method	SOLUTION SCATTERING
Organisms	Homo sapiens
Macromolecule	Apolipoprotein A-I (protein)
Unique Ligands	CLR, POV

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3MCB \| pdb_00003mcb	Download File View File

Crystal structure of NAC domains of human nascent polypeptide-associated complex (NAC)

Wang, L.F., Zhang, W.C., Wang, L., Zhang, X.J.C., Li, X.M., Rao, Z.

(2010) Protein Cell 1: 406-416

Released	2010-07-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Nascent polypeptide-associated complex subunit alpha (protein) Transcription factor BTF3 (protein)
Unique Ligands	IOD

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3MCE \| pdb_00003mce	Download File View File

Crystal structure of the NAC domain of alpha subunit of nascent polypeptide-associated complex(NAC)

Wang, L.F., Zhang, W.C., Wang, L., Zhang, X.J.C., Li, X.M., Rao, Z.

(2010) Protein Cell 1: 406-416

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.396 Å
Organisms	Homo sapiens
Macromolecule	Nascent polypeptide-associated complex subunit alpha (protein)
Unique Ligands	IOD

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3MTV \| pdb_00003mtv	Download File View File

The Crystal Structure of the PRRSV Nonstructural Protein Nsp1

Xue, F., Sun, Y.N., Yan, L.M., Zhao, C., Lou, Z.Y., Rao, Z.H.

(2010) J Virol 84: 6461-6471

Released	2010-05-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Porcine reproductive and respiratory syndrome virus
Macromolecule	Papain-like cysteine protease (protein)

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3NX1 \| pdb_00003nx1	Download File View File

Crystal structure of Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase

Gu, W., Yang, J.K., Lou, Z.Y., Meng, Z.H., Zhang, K.-Q.

(2011) PLoS One 6: e16262-e16262

Released	2011-02-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Enterobacter sp. Px6-4
Macromolecule	Ferulic acid decarboxylase (protein)

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3NX2 \| pdb_00003nx2	Download File View File

Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase in complex with substrate analogues

Gu, W., Yang, J.K., Lou, Z.Y., Meng, Z.H., Zhang, K.-Q.

(2011) PLoS One 6: e16262-e16262

Released	2011-02-16
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Enterobacter sp. Px6-4
Macromolecule	Ferulic acid decarboxylase (protein)
Unique Ligands	FER

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4PR3 \| pdb_00004pr3	Download File View File

Crystal structure of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

Zhang, X.C., Kang, X.S., Zhao, Y., Jiang, D.H., Li, X.M., Chen, Z.L.

(2014) Biochem Biophys Res Commun 446: 965-970

Released	2014-04-30
Method	X-RAY DIFFRACTION 2.606 Å
Organisms	Brucella melitensis bv. 1 str. 16M
Macromolecule	5'-methylthioadenosine nucleosidase / s-adenosylhomocysteine nucleosidase (protein)
Unique Ligands	ADE, GOL, PO4

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5YYF \| pdb_00005yyf	Download File View File

Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group

Li, Y., Li, H.

(2018) Nat Chem Biol 14: 1140-1149

Released	2018-11-07
Method	X-RAY DIFFRACTION 1.903 Å
Organisms	Homo sapiens
Macromolecule	Peptide inhibitor PHQ-H3(Q5-K9) (protein) Protein AF-9 (protein)
Unique Ligands	FOA, SO4

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6ISO \| pdb_00006iso	Download File View File

Human SIRT3 Recognizing H3K4cr

Wang, Y., Hao, Q.

(2014) Elife 3:

Released	2019-01-23
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	ARG-THR-LYS-GLN-THR-ALA-ARG (protein) NAD-dependent protein deacetylase sirtuin-3, mitochondrial (protein)
Unique Ligands	CRD, GOL, ZN

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6L5Z \| pdb_00006l5z	Download File View File

Crystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor

Li, Y., Chen, G., Li, H.

(2020) J Am Chem Soc 142: 21450-21459

Released	2020-10-28
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Protein AF-9 (protein) SC0-ALO-ALA-SC3-SC4-NH2 (protein)

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7CQ5 \| pdb_00007cq5	Download File View File

Structure of the human CLCN7-OSTM1 complex with ATP

Yang, G.H., Lu, Y.M., Zhang, Y.M., Jia, Y.T., Li, X.M., Lei, J.L.

To be published

Released	2020-11-11
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Homo sapiens
Macromolecule	H(+)/Cl(-) exchange transporter 7 (protein) Osteopetrosis-associated transmembrane protein 1 (protein)
Unique Ligands	ATP, CL
Unique branched monosaccharides	NAG

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7CQ6 \| pdb_00007cq6	Download File View File

Structure of the human CLCN7-OSTM1 complex

Yang, G.H., Lu, Y.M., Zhang, Y.M., Jia, Y.T., Li, X.M., Lei, J.L.

To be published

Released	2020-11-11
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens
Macromolecule	H(+)/Cl(-) exchange transporter 7 (protein) Osteopetrosis-associated transmembrane protein 1 (protein)
Unique Ligands	CL
Unique branched monosaccharides	NAG

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7CQ7 \| pdb_00007cq7	Download File View File

Structure of the human CLCN7-OSTM1 complex with ADP

Yang, G.H., Lu, Y.M., Zhang, Y.M., Jia, Y.T., Li, X.M., Lei, J.L.

To be published

Released	2020-11-11
Method	ELECTRON MICROSCOPY 3.55 Å
Organisms	Homo sapiens
Macromolecule	H(+)/Cl(-) exchange transporter 7 (protein) Osteopetrosis-associated transmembrane protein 1 (protein)
Unique Ligands	ADP, CL
Unique branched monosaccharides	NAG

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7XKJ \| pdb_00007xkj	Download File View File

Kras-G12D-GDP-MRTX1133 by FIB-MicroED

Li, X.M.

To be published

Released	2023-08-02
Method	ELECTRON CRYSTALLOGRAPHY 3 Å
Organisms	Homo sapiens
Macromolecule	KRAS proto-oncogene, GTPase (protein)
Unique Ligands	6IC, GDP, MG

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7XOU \| pdb_00007xou	Download File View File

Structural insights into human brain gut peptide cholecystokinin receptors

Ding, Y., Zhang, H., Liao, Y., Chen, L., Ji, S.

(2022) Cell Discov 8: 55-55

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 6

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7XOV \| pdb_00007xov	Download File View File

Structural insights into human brain gut peptide cholecystokinin receptors

Ding, Y., Zhang, H., Liao, Y., Chen, L., Ji, S.

(2022) Cell Discov 8: 55-55

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Cholecystokinin receptor type A (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (protein) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (protein) Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (protein) Nanobody 35 (protein)
Unique Ligands	IA1

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7XOW \| pdb_00007xow	Download File View File

Structural insights into human brain gut peptide cholecystokinin receptors

Ding, Y., Zhang, H., Liao, Y., Chen, L., Ji, S.

(2022) Cell Discov 8: 55-55

Released	2022-07-20
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6

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8IA7 \| pdb_00008ia7	Download File View File

Structural insights into human brain gut peptide cholecystokinin receptors

Ding, Y., Zhang, H., Liao, Y., Chen, L., Ji, S.

(2022) Cell Discov 8: 55-55

Released	2023-12-06
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6

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8WU1 \| pdb_00008wu1	Download File View File

Cryo-EM structure of CB1-beta-arrestin1 complex

Liao, Y., Zhang, H., Shen, Q., Cai, C.

(2023) Cell 186: 5784-5797.e17

Released	2024-03-20
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Beta-arrestin-1 (protein) Cannabinoid receptor 1,Vasopressin V2 receptor (protein) Fab30 heavy chain (protein) Fab30 light chain (protein)
Unique Ligands	KCA

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9K9R \| pdb_00009k9r	Download File View File

MPXV DNA polymerase in complex with primer/5U template DNA

Xie, Y.F., Kuai, L., Peng, Q., Wang, Q., Wang, H., Li, X.M., Qi, J.X., Ding, Q., Shi, Y., Gao, F.

To be published

Released	2025-03-05
Method	ELECTRON MICROSCOPY 2.61 Å
Organisms	Monkeypox virus
Macromolecule	DNA polymerase (protein) DNA polymerase processivity factor component A20 (protein) E4R (protein) DNA (25-MER) (nucleic acid) DNA (5U 38-MER) (nucleic acid)
Unique Ligands	MG, TTP

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9K9S \| pdb_00009k9s	Download File View File

MPXV DNA polymerase in complex with primer/4U template DNA

Xie, Y.F., Kuai, L., Peng, Q., Wang, Q., Wang, H., Li, X.M., Qi, J.X., Ding, Q., Shi, Y., Gao, F.

To be published

Released	2025-03-05
Method	ELECTRON MICROSCOPY 2.39 Å
Organisms	Monkeypox virus
Macromolecule	DNA polymerase (protein) DNA polymerase processivity factor component A20 (protein) E4R (protein) DNA (25-MER) (nucleic acid) DNA (4U 38-MER) (nucleic acid)
Unique Ligands	MG, TTP

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9K9T \| pdb_00009k9t	Download File View File

MPXV DNA polymerase in complex with CDV

Xie, Y.F., Kuai, L., Peng, Q., Wang, Q., Wang, H., Li, X.M., Qi, J.X., Ding, Q., Shi, Y., Gao, F.

To be published

Released	2025-03-05
Method	ELECTRON MICROSCOPY 2.96 Å
Organisms	Monkeypox virus
Macromolecule	DNA polymerase (protein) DNA polymerase processivity factor component A20 (protein) E4R (protein) DNA (24-MER) (nucleic acid) DNA (38-MER) (nucleic acid)

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9K9U \| pdb_00009k9u	Download File View File

MPXV DNA polymerase complex in editing state 1

Xie, Y.F., Kuai, L., Peng, Q., Wang, Q., Wang, H., Li, X.M., Qi, J.X., Ding, Q., Shi, Y., Gao, F.

To be published

Released	2025-02-26
Method	ELECTRON MICROSCOPY 3.08 Å
Organisms	Monkeypox virus
Macromolecule	DNA polymerase (protein) DNA polymerase processivity factor component A20 (protein) E4R (protein) DNA (25-MER) (nucleic acid) DNA (38-MER) (nucleic acid)

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9K9V \| pdb_00009k9v	Download File View File

MPXV DNA polymerase complex in editing state 2

Xie, Y.F., Kuai, L., Peng, Q., Wang, Q., Wang, H., Li, X.M., Qi, J.X., Ding, Q., Shi, Y., Gao, F.

To be published

Released	2025-03-05
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Monkeypox virus
Macromolecule	DNA polymerase (protein) DNA polymerase processivity factor (protein) Uracil-DNA glycosylase (protein) DNA (25-MER) (nucleic acid) DNA (38-MER) (nucleic acid)

1 to 24 of 24 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

3K2S | pdb_00003k2s

3MCB | pdb_00003mcb

3MCE | pdb_00003mce

3MTV | pdb_00003mtv

3NX1 | pdb_00003nx1

3NX2 | pdb_00003nx2

4PR3 | pdb_00004pr3

5YYF | pdb_00005yyf

6ISO | pdb_00006iso

6L5Z | pdb_00006l5z

7CQ5 | pdb_00007cq5

7CQ6 | pdb_00007cq6

7CQ7 | pdb_00007cq7

7XKJ | pdb_00007xkj

7XOU | pdb_00007xou

7XOV | pdb_00007xov

7XOW | pdb_00007xow

8IA7 | pdb_00008ia7

8WU1 | pdb_00008wu1

9K9R | pdb_00009k9r

9K9S | pdb_00009k9s

9K9T | pdb_00009k9t

9K9U | pdb_00009k9u

9K9V | pdb_00009k9v