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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "He, Y."

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Search Summary

This query matches 306 Structures.

Refinements

Structure Determination Methodology

experimental (306)

Scientific Name of Source Organism

	Homo sapiens (107)
	Saccharomyces cerevisiae S288C (19)
	Mus musculus (16)
	Lama glama (15)
	Bacteroides thetaiotaomicron VPI-5482 (14)
	Klebsiella pneumoniae (14)
	synthetic construct (14)
	Methanococcus voltae (13)
	Bos taurus (9)
	Severe acute respiratory syndrome coronavirus 2 (9)

More...

Taxonomy

	Eukaryota (174)
	Bacteria (86)
	Riboviria (33)
	Archaea (17)
	other sequences (14)
	Duplodnaviria (7)
	Eukaryota (eukaryotes) (3)
	Riboviria (RNA viruses and viroids) (1)

Experimental Method

	X-RAY DIFFRACTION (142)
	ELECTRON MICROSCOPY (127)
	SOLUTION NMR (37)

Polymer Entity Type

	Protein (301)
	DNA (37)
	RNA (21)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (43)
	2.0 - 2.5 (53)
	2.5 - 3.0 (46)
	3.0 - 3.5 (53)
	3.5 - 4.0 (32)
	4.0 - 4.5 (9)
	> 4.5 (28)

Release Date

	2000 - 2004 (13)
	2005 - 2009 (43)
	2010 - 2014 (41)
	2015 - 2019 (66)
	2020 - 2024 (134)
	2025 - 2029 (9)

Enzyme Classification Name

	Hydrolases (104)
	Transferases (45)
	Isomerases (10)
	Ligases (7)
	Translocases (8)
	Lyases (5)
	Oxidoreductases (3)

Membrane Protein Annotation

	PDBTM (56)
	MemProtMD (32)
	mpstruc (31)
	OPM (28)

Symmetry Type

	Asymmetric (221)
	Cyclic (71)
	Icosahedral (13)
	Dihedral (2)

SCOP Classification

	Alpha and beta proteins (a/b) (29)
	Multi-domain proteins (alpha and beta) (6)
	All alpha proteins (31)
	Alpha and beta proteins (a+b) (26)
	Low resolution protein structures (4)
	Artifacts (8)
	All beta proteins (7)

AllSelected

1 to 25 of 306 Structures

Page 1 of 13

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1DGI \| pdb_00001dgi	Download File View File

Cryo-EM structure of human poliovirus(serotype 1)complexed with three domain CD155

He, Y., Bowman, V.D., Mueller, S., Bator, C.M., Bella, J., Peng, X., Baker, T.S., Wimmer, E., Kuhn, R.J., Rossmann, M.G.

(2000) Proc Natl Acad Sci U S A 97: 79-84

Released	2000-01-24
Method	ELECTRON MICROSCOPY 22 Å
Organisms	Homo sapiens Poliovirus 1
Macromolecule	POLIOVIRUS RECEPTOR (protein) VP1 (protein) VP2 (protein) VP3 (protein) VP4 (protein)

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1FOQ \| pdb_00001foq	Download File View File

PENTAMERIC MODEL OF THE BACTERIOPHAGE PHI29 PROHEAD RNA

Simpson, A.A., Tao, Y., Leiman, P.G., Badasso, M.O., He, Y., Jardine, P.J., Olson, N.H., Morais, M.C., Grimes, S., Anderson, D.L., Baker, T.S., Rossmann, M.G.

(2000) Nature 408: 745-750

Released	2000-12-22
Method	ELECTRON MICROSCOPY 20 Å
Organisms	Salasvirus phi29
Macromolecule	BACTERIOPHAGE PHI29 PROHEAD RNA (nucleic acid)

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1FOU \| pdb_00001fou	Download File View File

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

Simpson, A.A., Tao, Y., Leiman, P.G., Badasso, M.O., He, Y., Jardine, P.J., Olson, N.H., Morais, M.C., Grimes, S.N., Anderson, D.L., Baker, T.S., Rossmann, M.G.

(2000) Nature 408: 745-750

Released	2000-12-22
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Salasvirus phi29
Macromolecule	UPPER COLLAR PROTEIN (protein)

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1IJG \| pdb_00001ijg	Download File View File

Structure of the Bacteriophage phi29 Head-Tail Connector Protein

Simpson, A.A., Leiman, P.G., Tao, Y., He, Y., Badasso, M., Jardine, P.J., Anderson, D.L., Rossmann, M.G.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1260-1269

Released	2001-05-09
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Salasvirus phi29
Macromolecule	UPPER COLLAR PROTEIN (protein)

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1JEW \| pdb_00001jew	Download File View File

CRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR, COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (CAR).

Rossmann, M.G., He, Y.

(2001) Nat Struct Biol 8: 874-878

Released	2001-10-03
Method	ELECTRON MICROSCOPY 22 Å
Organisms	Coxsackievirus B3 (strain Woodruff) Homo sapiens
Macromolecule	COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (protein) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 (protein) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 (protein) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 (protein) COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 (protein)

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1JM4 \| pdb_00001jm4	Download File View File

NMR Structure of P/CAF Bromodomain in Complex with HIV-1 Tat Peptide

Mujtaba, S., He, Y., Zeng, L., Farooq, A., Carlson, J.E., Ott, M., Verdin, E., Zhou, M.-M.

(2002) Mol Cell 9: 575-586

Released	2002-07-17
Method	SOLUTION NMR
Organisms	Homo sapiens Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)
Macromolecule	HIV-1 Tat Peptide (protein) P300/CBP-associated Factor (protein)

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1JNB \| pdb_00001jnb	Download File View File

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

Simpson, A.A., Leiman, P.G., Tao, Y., He, Y., Badasso, M.O., Jardine, P.J., Anderson, D.L., Rossmann, M.G.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1260-1269

Released	2001-08-15
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Salasvirus phi29
Macromolecule	UPPER COLLAR PROTEIN (protein)

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1JSP \| pdb_00001jsp	Download File View File

NMR Structure of CBP Bromodomain in complex with p53 peptide

He, Y., Mujtaba, S., Zeng, L., Yan, S., Zhou, M.-M.

(2004) Mol Cell 13: 251-263

Released	2002-08-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	CREB-BINDING PROTEIN (protein) tumor protein p53 (protein)

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1M11 \| pdb_00001m11	Download File View File

structural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy

He, Y., Lin, F., Chipman, P.R., Bator, C.M., Baker, T.S., Shoham, M., Kuhn, R.J., Medof, M.E., Rossmann, M.G.

(2002) Proc Natl Acad Sci U S A 99: 10325-10329

Released	2002-08-28
Method	ELECTRON MICROSCOPY 16 Å
Organisms	Echovirus E7 Homo sapiens
Macromolecule	COAT PROTEIN VP1 (protein) COAT PROTEIN VP2 (protein) COAT PROTEIN VP3 (protein) decay-accelerating factor (protein)

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1NN8 \| pdb_00001nn8	Download File View File

CryoEM structure of poliovirus receptor bound to poliovirus

He, Y., Mueller, S., Chipman, P.R., Bator, C.M., Peng, X., Bowman, V.D., Mukhopadhyay, S., Wimmer, E., Kuhn, R.J., Rossmann, M.G.

(2003) J Virol 77: 4827-4835

Released	2004-01-27
Method	ELECTRON MICROSCOPY 15 Å
Organisms	Homo sapiens Human poliovirus 1 Mahoney
Macromolecule	coat protein VP1 (protein) coat protein VP2 (protein) coat protein VP3 (protein) coat protein VP4 (protein) poliovirus receptor (protein)
Unique Ligands	MYR

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1S17 \| pdb_00001s17	Download File View File

Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors

Molteni, V., He, X., Nabakka, J., Yang, K., Kreusch, A., Gordon, P., Bursulaya, B., Ryder, N.S., Goldberg, R., He, Y.

(2004) Bioorg Med Chem Lett 14: 1477-1481

Released	2004-03-30
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Peptide deformylase (protein)
Unique Ligands	GNR, GOL, NI

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1T4G \| pdb_00001t4g	Download File View File

ATPase in complex with AMP-PNP

Wu, Y., He, Y., Moya, I.A., Qian, X., Luo, Y.

(2004) Mol Cell 15: 423-435

Released	2004-08-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, MG

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1XU4 \| pdb_00001xu4	Download File View File

ATPASE IN COMPLEX WITH AMP-PNP, MAGNESIUM AND POTASSIUM CO-F

Wu, Y., Qian, X., He, Y., Moya, I.A., Luo, Y.

(2005) J Biological Chem 280: 722-728

Released	2004-11-16
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, K, MG

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1YC1 \| pdb_00001yc1	Download File View File

Crystal Structures of human HSP90alpha complexed with dihydroxyphenylpyrazoles

Kreusch, A., Han, S., Brinker, A., Zhou, V., Choi, H., He, Y., Lesley, S.A., Caldwell, J., Gu, X.

(2005) Bioorg Med Chem Lett 15: 1475-1478

Released	2005-02-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Heat shock protein HSP 90-alpha (protein)
Unique Ligands	4BC

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1YC3 \| pdb_00001yc3	Download File View File

Crystal Structure of human HSP90alpha complexed with dihydroxyphenylpyrazoles

Kreusch, A., Han, S., Brinker, A., Zhou, V., Choi, H., He, Y., Lesley, S.A., Caldwell, J., Gu, X.

(2005) Bioorg Med Chem Lett 15: 1475-1478

Released	2005-02-22
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Homo sapiens
Macromolecule	Heat shock protein HSP 90-alpha (protein)
Unique Ligands	4BC

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1YC4 \| pdb_00001yc4	Download File View File

Crystal structure of human HSP90alpha complexed with dihydroxyphenylpyrazoles

Kreusch, A., Han, S., Brinker, A., Zhou, V., Choi, H., He, Y., Lesley, S.A., Caldwell, J., Gu, X.

(2005) Bioorg Med Chem Lett 15: 1475-1478

Released	2005-02-22
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	Heat shock protein HSP 90-alpha (protein)
Unique Ligands	43P

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1ZXG \| pdb_00001zxg	Download File View File

Solution structure of A219

He, Y., Yeh, D.C., Alexander, P., Bryan, P.N., Orban, J.

(2005) Biochemistry 44: 14055-14061

Released	2005-11-08
Method	SOLUTION NMR
Organisms	Staphylococcus aureus
Macromolecule	Immunoglobulin G binding protein A (protein)

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1ZXH \| pdb_00001zxh	Download File View File

G311 mutant protein

He, Y., Yeh, D.C., Alexander, P., Bryan, P.N., Orban, J.

(2005) Biochemistry 44: 14055-14061

Released	2005-11-08
Method	SOLUTION NMR
Organisms	Streptococcus sp.
Macromolecule	Immunoglobulin G binding protein G (protein)

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2APN \| pdb_00002apn	Download File View File

hi1723 solution structure

He, Y., Yeh, D.C., Orban, J., Structure 2 Function Project (S2F)

To be published

Released	2006-10-03
Method	SOLUTION NMR
Organisms	Haemophilus influenzae
Macromolecule	Protein HI1723 (protein)

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2B21 \| pdb_00002b21	Download File View File

RADA Recombinase in complex with AMPPNP at pH 6.0

Qian, X., He, Y., Wu, Y., Luo, Y.

To be published

Released	2006-08-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, K, MG

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2F1H \| pdb_00002f1h	Download File View File

RECOMBINASE IN COMPLEX WITH AMP-PNP and Potassium

Qian, X., He, Y., Wu, Y., Luo, Y.

(2006) J Mol Biology 360: 537-547

Released	2006-05-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, K, MG

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2F1I \| pdb_00002f1i	Download File View File

Recombinase in Complex with AMP-PNP

Qian, X., He, Y., Wu, Y., Luo, Y.

(2006) J Mol Biology 360: 537-547

Released	2006-05-30
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, MG

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2F1J \| pdb_00002f1j	Download File View File

Recombinase in Complex with ADP

Qian, X., He, Y., Wu, Y., Luo, Y.

(2006) J Mol Biology 360: 537-547

Released	2006-05-30
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ADP, MG

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2FPK \| pdb_00002fpk	Download File View File

RadA recombinase in complex with ADP

Wu, Y., Qian, X., He, Y., Moya, I.A., Luo, Y.

(2005) Biochemistry 44: 13753-13761

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ADP, K, MG

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2FPL \| pdb_00002fpl	Download File View File

RadA recombinase in complex with AMP-PNP and low concentration of K+

Wu, Y., Qian, X., He, Y., Moya, I.A., Luo, Y.

(2005) Biochemistry 44: 13753-13761

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Methanococcus voltae
Macromolecule	DNA repair and recombination protein radA (protein)
Unique Ligands	ANP, K, MG

1 to 25 of 306 Structures

Page 1 of 13

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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

1DGI | pdb_00001dgi

1FOQ | pdb_00001foq

1FOU | pdb_00001fou

1IJG | pdb_00001ijg

1JEW | pdb_00001jew

1JM4 | pdb_00001jm4

1JNB | pdb_00001jnb

1JSP | pdb_00001jsp

1M11 | pdb_00001m11

1NN8 | pdb_00001nn8

1S17 | pdb_00001s17

1T4G | pdb_00001t4g

1XU4 | pdb_00001xu4

1YC1 | pdb_00001yc1

1YC3 | pdb_00001yc3

1YC4 | pdb_00001yc4

1ZXG | pdb_00001zxg

1ZXH | pdb_00001zxh

2APN | pdb_00002apn

2B21 | pdb_00002b21

2F1H | pdb_00002f1h

2F1I | pdb_00002f1i

2F1J | pdb_00002f1j

2FPK | pdb_00002fpk

2FPL | pdb_00002fpl