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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Ni, X."

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Search Summary

This query matches 785 Structures.

Refinements

Structure Determination Methodology

experimental (785)

Scientific Name of Source Organism

	Coxsackievirus A16 (284)
	Chikungunya virus (133)
	Zika virus (123)
	enterovirus D68 (104)
	Severe acute respiratory syndrome coronavirus 2 (99)
	Homo sapiens (21)
	Mus musculus (7)
	Thermothelomyces thermophilus (6)
	Bacillus subtilis (2)
	Enterovirus (2)

More...

Taxonomy

	Riboviria (749)
	Eukaryota (34)
	Bacteria (2)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (773)
	ELECTRON MICROSCOPY (12)

Polymer Entity Type

	Protein (785)
	DNA (5)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (450)
	1.5 - 2.0 (277)
	2.0 - 2.5 (36)
	2.5 - 3.0 (10)
	3.0 - 3.5 (8)
	3.5 - 4.0 (3)
	> 4.5 (1)

Release Date

	2010 - 2014 (7)
	2015 - 2019 (5)
	2020 - 2024 (533)
	2025 - 2029 (240)

Enzyme Classification Name

	Hydrolases (750)
	Transferases (8)

Membrane Protein Annotation

	PDBTM (6)
	mpstruc (6)
	OPM (4)

Symmetry Type

	Asymmetric (769)
	Cyclic (16)

SCOP Classification

	Artifacts (12)
	Alpha and beta proteins (a/b) (7)
	All beta proteins (4)
	Alpha and beta proteins (a+b) (3)
	All alpha proteins (1)

AllSelected

1 to 25 of 785 Structures

Page 1 of 32

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4JBJ \| pdb_00004jbj	Download File View File

Structural mimicry for functional antagonism

Ru, H., Ni, X., Ma, F., Zhao, L., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

(2013) Cell Res 23: 855-858

Released	2013-06-26
Method	X-RAY DIFFRACTION 2.692 Å
Organisms	Mus musculus
Macromolecule	Interferon-activable protein 202 (protein)

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4JBK \| pdb_00004jbk	Download File View File

Molecular basis for abrogation of activation of pro-inflammatory cytokines

Ru, H., Ni, X., Crowley, C., Zhao, L., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

(2013) Cell Res 23: 855-858

Released	2013-06-26
Method	X-RAY DIFFRACTION 2.963 Å
Organisms	Mus musculus
Macromolecule	Interferon-activable protein 202 (protein) DNA (5'-D(PGPGPAPAPTPTPAPTPAPAPTPTPCPC)-3') (nucleic acid)

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4JBM \| pdb_00004jbm	Download File View File

Structure of murine DNA binding protein bound with ds DNA

Ru, H., Ni, X., Crowley, C., Zhao, L., Ding, W., Hung, L.-W., Shaw, N., Cheng, G., Liu, Z.-J.

(2013) Cell Res 23: 855-858

Released	2013-06-26
Method	X-RAY DIFFRACTION 2.218 Å
Organisms	Mus musculus
Macromolecule	Interferon-inducible protein AIM2 (protein) DNA (5'-D(GPGPCPGPCPGPCPGPCPGPCPC)-3') (nucleic acid)

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4NOJ \| pdb_00004noj	Download File View File

Crystal structure of the mature form of asparaginyl endopeptidase (AEP)/Legumain activated at pH 3.5

Zhao, L., Hua, T., Ru, H., Ni, X., Shaw, N., Jiao, L., Ding, W., Qu, L., Ouyang, S., Liu, Z.J.

(2014) Cell Res 24: 344-358

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus
Macromolecule	Legumain (protein)

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4NOK \| pdb_00004nok	Download File View File

Crystal structure of proenzyme asparaginyl endopeptidase (AEP)/Legumain at pH 7.5

Zhao, L., Hua, T., Ru, H., Ni, X., Shaw, N., Jiao, L., Ding, W., Qu, L., Ouyang, S., Liu, Z.J.

(2014) Cell Res 24: 344-358

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus
Macromolecule	Legumain (protein)

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4NOL \| pdb_00004nol	Download File View File

Crystal structure of proenzyme asparaginyl endopeptidase (AEP)/Legumain mutant D233A at pH 7.5

Zhao, L., Hua, T., Ru, H., Ni, X., Shaw, N., Jiao, L., Ding, W., Qu, L., Ouyang, S., Liu, Z.J.

(2014) Cell Res 24: 344-358

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	Legumain (protein)

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4NOM \| pdb_00004nom	Download File View File

Crystal structure of asparaginyl endopeptidase (AEP)/Legumain activated at pH 4.5

Zhao, L., Hua, T., Ru, H., Ni, X., Shaw, N., Jiao, L., Ding, W., Qu, L., Ouyang, S., Liu, Z.J.

(2014) Cell Res 24: 344-358

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.006 Å
Organisms	Mus musculus
Macromolecule	Legumain (protein)

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4QGU \| pdb_00004qgu	Download File View File

protein domain complex with ssDNA

Ni, X., Ru, H., Zhao, L., Shaw, N., Ding, W., Songying, O., Liu, Z.-J.

(2016) J Mol Cell Biol 8: 51-61

Released	2015-06-17
Method	X-RAY DIFFRACTION 2.545 Å
Organisms	Homo sapiens
Macromolecule	Gamma-interferon-inducible protein 16 (protein) DNA (5'-D(PAPGPGPCPCPGPGPCPGPTPGPA)-3') (nucleic acid)

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6OSL \| pdb_00006osl	Download File View File

Cryo-EM structure of the N-terminally acetylated C-terminal Alpha-synuclein truncation Ac1-122

Ni, X., McGlinchey, R.P., Jiang, J., Lee, J.C.

(2019) J Mol Biology 431: 3913-3919

Released	2019-09-25
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens
Macromolecule	Alpha-synuclein (protein)

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6PPF \| pdb_00006ppf	Download File View File

Bacterial 45SRbgA ribosomal particle class B

Ortega, J., Seffouh, A., Jain, N., Jahagirdar, D., Basu, K., Razi, A., Ni, X., Guarne, A., Britton, R.A.

(2019) Nucleic Acids Res 47: 10414-10425

Released	2019-09-18
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Bacillus subtilis
Macromolecule	Unique protein chains: 19 Unique nucleic acid chains: 2

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6PVK \| pdb_00006pvk	Download File View File

Bacterial 45SRbgA ribosomal particle class A

Ortega, J., Seffouh, A., Jain, N., Jahagirdar, D., Basu, K., Razi, A., Ni, X., Guarne, A., Britton, R.A.

(2019) Nucleic Acids Res 47: 10414-10425

Released	2019-09-18
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Bacillus subtilis
Macromolecule	Unique protein chains: 16 Unique nucleic acid chains: 1

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6T6B \| pdb_00006t6b	Download File View File

Crystal structure of PPARgamma in complex with compound 16 (MF27)

Chaikuad, A., Ni, X., Hanke, T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Merk, D., Knapp, S., Structural Genomics Consortium (SGC)

(2020) J Med Chem 63: 4555-4561

Released	2019-12-11
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Peroxisome proliferator-activated receptor gamma (protein)
Unique Ligands	MLQ

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6WUH \| pdb_00006wuh	Download File View File

Mitochondrial SAM complex in lipid nanodiscs

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein) Tom37 domain-containing protein (protein)

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6WUJ \| pdb_00006wuj	Download File View File

Mitochondrial SAM complex - monomer in detergent

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein) Tom37 domain-containing protein (protein)

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6WUL \| pdb_00006wul	Download File View File

Mitochondrial SAM complex - dimer 1 in detergent

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein) Tom37 domain-containing protein (protein)

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6WUM \| pdb_00006wum	Download File View File

Mitochondrial SAM complex - dimer 2 in detergent

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein) Tom37 domain-containing protein (protein)

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6WUN \| pdb_00006wun	Download File View File

Mitochondrial SAM complex - dimer 3 in detergent

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein)

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6WUT \| pdb_00006wut	Download File View File

Mitochondrial SAM complex - high resolution monomer in detergent

Ni, X., Botos, I., Diederichs, K.

(2020) Nat Commun 11: 3290-3290

Released	2020-08-12
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Thermothelomyces thermophilus
Macromolecule	Bac_surface_Ag domain-containing protein (protein) Sam35 (protein) Tom37 domain-containing protein (protein)

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6Y24 \| pdb_00006y24	Download File View File

Crystal structure of fourth KH domain of FUBP1

Ni, X., Joerger, A.C., Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

(2020) Sci Rep 10: 13459-13459

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Homo sapiens
Macromolecule	Far upstream element-binding protein 1 (protein)
Unique Ligands	EDO

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6Y2C \| pdb_00006y2c	Download File View File

Crystal structure of the third KH domain of FUBP1

Ni, X., Joerger, A.C., Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

(2020) Sci Rep 10: 13459-13459

Released	2020-03-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Far upstream element-binding protein 1 (protein)
Unique Ligands	EDO, ZN

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6Y2D \| pdb_00006y2d	Download File View File

Crystal structure of the second KH domain of FUBP1

Ni, X., Chaikuad, A., Joerger, A.C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

(2020) Sci Rep 10: 13459-13459

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Far upstream element-binding protein 1 (protein)
Unique Ligands	GOL, SO4

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6YWK \| pdb_00006ywk	Download File View File

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES

Ni, X., Schroeder, M., Olieric, V., Sharpe, E.M., Wojdyla, J.A., Wang, M., Knapp, S., Chaikuad, A., Structural Genomics Consortium (SGC)

(2021) ACS Med Chem Lett 12: 603-609

Released	2020-05-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	NSP3 macrodomain (protein)
Unique Ligands	EDO, EPE, MG

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6YWL \| pdb_00006ywl	Download File View File

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose

Schroeder, M., Ni, X., Olieric, V., Sharpe, E.M., Wojdyla, J.A., Wang, M., Knapp, S., Chaikuad, A., Structural Genomics Consortium (SGC)

(2021) ACS Med Chem Lett 12: 603-609

Released	2020-05-06
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	NSP3 macrodomain (protein)
Unique Ligands	APR, EDO, MG

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6YWM \| pdb_00006ywm	Download File View File

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with MES

Ni, X., Schroeder, M., Olieric, V., Sharpe, E.M., Wojdyla, J.A., Wang, M., Knapp, S., Chaikuad, A., Structural Genomics Consortium (SGC)

(2021) ACS Med Chem Lett 12: 603-609

Released	2020-05-06
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	NSP3 macrodomain (protein)
Unique Ligands	EDO, MES, MG