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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yao, T."

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Search Summary

This query matches 35 Structures.

Refinements

Structure Determination Methodology

experimental (35)

Scientific Name of Source Organism

	Homo sapiens (30)
	Xenopus laevis (6)
	synthetic construct (6)
	Mus musculus (4)
	Candida albicans (2)
	Saccharomyces cerevisiae (2)
	Thermus thermophilus (1)
	Thermus thermophilus HB8 (1)

Taxonomy

	Eukaryota (33)
	other sequences (6)
	Bacteria (2)

Experimental Method

	X-RAY DIFFRACTION (29)
	ELECTRON MICROSCOPY (6)

Polymer Entity Type

	Protein (35)
	DNA (8)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (11)
	2.0 - 2.5 (9)
	2.5 - 3.0 (4)
	3.0 - 3.5 (4)
	4.0 - 4.5 (4)
	> 4.5 (1)

Release Date

	2000 - 2004 (2)
	2005 - 2009 (2)
	2010 - 2014 (5)
	2015 - 2019 (16)
	2020 - 2024 (7)
	2025 - 2029 (3)

Enzyme Classification Name

	Transferases (20)
	Hydrolases (9)
	Oxidoreductases (2)

Symmetry Type

	Asymmetric (31)
	Cyclic (5)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a+b) (10)
	All alpha proteins (5)
	Artifacts (3)

AllSelected

1 to 25 of 35 Structures

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1NB8 \| pdb_00001nb8	Download File View File

Structure of the catalytic domain of USP7 (HAUSP)

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1NBF \| pdb_00001nbf	Download File View File

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin aldehyde (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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2DQ4 \| pdb_00002dq4	Download File View File

Crystal structure of threonine 3-dehydrogenase

Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-06-12
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	L-threonine 3-dehydrogenase (protein)
Unique Ligands	MES, ZN

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2EJV \| pdb_00002ejv	Download File View File

Crystal structure of threonine 3-dehydrogenase complexed with NAD+

Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K.

To be published

Released	2008-03-25
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Thermus thermophilus HB8
Macromolecule	L-threonine 3-dehydrogenase (protein)
Unique Ligands	NAD, ZN

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3MHH \| pdb_00003mhh	Download File View File

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module

Samara, N.L., Datta, A.B., Berndsen, C.E., Zhang, X., Yao, T., Cohen, R.E., Wolberger, C.

(2010) Science 328: 1025-1029

Released	2010-04-21
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein SUS1 (protein) SAGA-associated factor 11 (protein) SAGA-associated factor 73 (protein) Ubiquitin carboxyl-terminal hydrolase 8 (protein)
Unique Ligands	ZN

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3MHS \| pdb_00003mhs	Download File View File

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde

Samara, N.L., Datta, A.B., Berndsen, C.E., Zhang, X., Yao, T., Cohen, R.E., Wolberger, C.

(2010) Science 328: 1025-1029

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Protein SUS1 (protein) SAGA-associated factor 11 (protein) SAGA-associated factor 73 (protein) Ubiquitin (protein) Ubiquitin carboxyl-terminal hydrolase 8 (protein)
Unique Ligands	EDO, GOL, ZN

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3QRI \| pdb_00003qri	Download File View File

The crystal structure of human abl1 kinase domain in complex with DCC-2036

Chan, W.W., Wise, S.C., Kaufman, M.D., Ahn, Y.M., Ensinger, C.L., Haack, T., Hood, M.M., Jones, J., Lord, J.W., Lu, W.P., Miller, D., Patt, W.C., Smith, B.D., Petillo, P.A., Rutkoski, T.J., Telikepalli, H., Vogeti, L., Yao, T., Chun, L., Clark, R., Evangelista, P., Gavrilescu, L.C., Lazarides, K., Zaleskas, V.M., Stewart, L.J., Van Etten, R.A., Flynn, D.L.

(2011) Cancer Cell 19: 556-568

Released	2011-06-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase ABL1 (protein)
Unique Ligands	919, NA

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3QRJ \| pdb_00003qrj	Download File View File

The crystal structure of human abl1 kinase domain T315I mutant in complex with DCC-2036

(2011) Cancer Cell 19: 556-568

Released	2011-06-01
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase ABL1 (protein)
Unique Ligands	919

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3QRK \| pdb_00003qrk	Download File View File

The crystal structure of human abl1 kinase domain in complex with DP-987

(2011) Cancer Cell 19: 556-568

Released	2011-06-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Tyrosine-protein kinase ABL1 (protein)
Unique Ligands	9DP

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4WLP \| pdb_00004wlp	Download File View File

Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex

Hemmis, C.W., Hill, C.P., VanderLinden, R., Whitby, F.G.

(2015) Mol Cell 57: 901-911

Released	2015-03-04
Method	X-RAY DIFFRACTION 3.102 Å
Organisms	Homo sapiens
Macromolecule	Nuclear factor related to kappa-B-binding protein (protein) Ubiquitin carboxyl-terminal hydrolase isozyme L5 (protein)

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4WLQ \| pdb_00004wlq	Download File View File

Crystal structure of mUCH37-hRPN13 CTD complex

Hemmis, C.W., Hill, C.P., VanderLinden, R., Whitby, F.G.

(2015) Mol Cell 57: 901-911

Released	2015-03-04
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Proteasomal ubiquitin receptor ADRM1 (protein) Ubiquitin carboxyl-terminal hydrolase isozyme L5 (protein)

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4WLR \| pdb_00004wlr	Download File View File

Crystal Structure of mUCH37-hRPN13 CTD-hUb complex

Hemmis, C.W., Hill, C.P., VanderLinden, R., Whitby, F.G.

(2015) Mol Cell 57: 901-911

Released	2015-03-04
Method	X-RAY DIFFRACTION 1.997 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Polyubiquitin-B (protein) Proteasomal ubiquitin receptor ADRM1 (protein) Ubiquitin carboxyl-terminal hydrolase isozyme L5 (protein)

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5B1L \| pdb_00005b1l	Download File View File

The mouse nucleosome structure containing H3t

Urahama, T., Machida, S., Horikoshi, N., Osakabe, A., Tachiwana, H., Taguchi, H., Kurumizaka, H.

(2017) Cell Rep 18: 593-600

Released	2017-02-15
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Histone H2A type 1 (protein) Histone H2B type 3-A (protein) Histone H3t (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)
Unique Ligands	CL, MN

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5B1M \| pdb_00005b1m	Download File View File

The mouse nucleosome structure containing H3.1

Urahama, T., Machida, S., Horikoshi, N., Osakabe, A., Tachiwana, H., Taguchi, H., Kurumizaka, H.

(2017) Cell Rep 18: 593-600

Released	2017-02-15
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Histone H2A type 1 (protein) Histone H2B type 3-A (protein) Histone H3.1 (protein) Histone H4 (protein) DNA (146-MER) (nucleic acid)

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5V1Y \| pdb_00005v1y	Download File View File

Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Hemmis, C.W., VanderLinden, R.T., Yao, T., Robinson, H., Hill, C.P.

(2017) J Biological Chem 292: 9493-9504

Released	2017-05-03
Method	X-RAY DIFFRACTION 1.421 Å
Organisms	Homo sapiens
Macromolecule	26S proteasome non-ATPase regulatory subunit 1 (protein) Proteasomal ubiquitin receptor ADRM1 (protein) Ubiquitin (protein)

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5V1Z \| pdb_00005v1z	Download File View File

Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex

Hemmis, C.W., VanderLinden, R.T., Yao, T., Robinson, H., Hill, C.P.

(2017) J Biological Chem 292: 9493-9504

Released	2017-05-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	26S proteasome non-ATPase regulatory subunit 1 (protein) Proteasomal ubiquitin receptor ADRM1 (protein) Ubiquitin (protein)

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6B3E \| pdb_00006b3e	Download File View File

Crystal structure of human CDK12/CyclinK in complex with an inhibitor

Ferguson, A.D.

(2018) ChemMedChem 13: 231-235

Released	2017-12-27
Method	X-RAY DIFFRACTION 3.06 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-K (protein) Cyclin-dependent kinase 12 (protein)
Unique Ligands	CJM, EDO, MG

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6CPT \| pdb_00006cpt	Download File View File

crystal structure of yeast caPDE2 in complex with IBMX

Ke, h., Wang, Y.

(2018) Biochemistry 57: 6070-6077

Released	2019-02-20
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Candida albicans
Macromolecule	Phosphodiesterase (protein)
Unique Ligands	IBM, MG, ZN

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6CPU \| pdb_00006cpu	Download File View File

Crystal structure of yeast caPDE2

Ke, H., Wang, y.

(2018) Biochemistry 57: 6070-6077

Released	2019-02-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Candida albicans
Macromolecule	Phosphodiesterase (protein)
Unique Ligands	MG, ZN

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6J99 \| pdb_00006j99	Download File View File

Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome

Yao, T., Huang, J.

(2019) Cell Res 29: 330-333

Released	2019-02-27
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2
Unique Ligands	SAH

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6KIU \| pdb_00006kiu	Download File View File

Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)

Huang, J., Xue, H., Yao, T.

(2019) Nature 573: 445-449

Released	2019-09-11
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 9 Unique nucleic acid chains: 2
Unique Ligands	GLN, LYS, SAH, ZN

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6KIV \| pdb_00006kiv	Download File View File

Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom)

Huang, J., Xue, H., Yao, T.

(2019) Nature 573: 445-449

Released	2019-09-11
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 9 Unique nucleic acid chains: 2
Unique Ligands	SAH, ZN

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6KIW \| pdb_00006kiw	Download File View File

Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)

Huang, J., Xue, H., Yao, T.

(2019) Nature 573: 445-449

Released	2019-09-11
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 9 Unique nucleic acid chains: 2
Unique Ligands	ZN

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6KIX \| pdb_00006kix	Download File View File

Cryo-EM structure of human MLL1-NCP complex, binding mode1

Huang, J., Xue, H., Yao, T.

(2019) Nature 573: 445-449

Released	2019-09-11
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 8 Unique nucleic acid chains: 2
Unique Ligands	GLN, LYS, SAH, ZN

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6KIZ \| pdb_00006kiz	Download File View File

Cryo-EM structure of human MLL1-NCP complex, binding mode2

Huang, J., Xue, H., Yao, T.

(2019) Nature 573: 445-449

Released	2019-09-11
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 8 Unique nucleic acid chains: 2
Unique Ligands	SAH, ZN

1 to 25 of 35 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

Symmetry Type

SCOP Classification

1NB8 | pdb_00001nb8

1NBF | pdb_00001nbf

2DQ4 | pdb_00002dq4

2EJV | pdb_00002ejv

3MHH | pdb_00003mhh

3MHS | pdb_00003mhs

3QRI | pdb_00003qri

3QRJ | pdb_00003qrj

3QRK | pdb_00003qrk

4WLP | pdb_00004wlp

4WLQ | pdb_00004wlq

4WLR | pdb_00004wlr

5B1L | pdb_00005b1l

5B1M | pdb_00005b1m

5V1Y | pdb_00005v1y

5V1Z | pdb_00005v1z

6B3E | pdb_00006b3e

6CPT | pdb_00006cpt

6CPU | pdb_00006cpu

6J99 | pdb_00006j99

6KIU | pdb_00006kiu

6KIV | pdb_00006kiv

6KIW | pdb_00006kiw

6KIX | pdb_00006kix

6KIZ | pdb_00006kiz