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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ren, Y."

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Search Summary

This query matches 188 Structures.

Refinements

Structure Determination Methodology

experimental (188)

Scientific Name of Source Organism

	Homo sapiens (105)
	Sus scrofa (26)
	Severe acute respiratory syndrome coronavirus 2 (22)
	synthetic construct (22)
	Amanita phalloides (16)
	Saccharomyces cerevisiae (10)
	Mus musculus (7)
	Bos taurus (6)
	Danio rerio (6)
	Vicugna pacos (6)

More...

Taxonomy

	Eukaryota (157)
	Riboviria (32)
	other sequences (22)
	Bacteria (13)
	Duplodnaviria (3)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (96)
	ELECTRON MICROSCOPY (92)

Polymer Entity Type

	Protein (175)
	DNA (45)
	RNA (29)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (24)
	2.0 - 2.5 (33)
	2.5 - 3.0 (41)
	3.0 - 3.5 (42)
	3.5 - 4.0 (19)
	4.0 - 4.5 (5)
	> 4.5 (19)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (4)
	2010 - 2014 (17)
	2015 - 2019 (10)
	2020 - 2024 (143)
	2025 - 2029 (11)

Enzyme Classification Name

	Transferases (46)
	Hydrolases (62)
	Isomerases (12)
	Lyases (5)
	Oxidoreductases (2)

Membrane Protein Annotation

	PDBTM (18)
	mpstruc (14)
	MemProtMD (15)
	OPM (8)

Symmetry Type

	Asymmetric (123)
	Cyclic (43)
	Dihedral (6)
	Icosahedral (3)

SCOP Classification

	All alpha proteins (3)
	Artifacts (3)
	Alpha and beta proteins (a+b) (9)
	Alpha and beta proteins (a/b) (4)
	Multi-domain proteins (alpha and beta) (6)
	All beta proteins (1)

AllSelected

1 to 25 of 188 Structures

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1N4E \| pdb_00001n4e	Download File View File

Crystal Structure of a DNA Decamer Containing a Thymine-dimer

Park, H., Zhang, K., Ren, Y., Nadji, S., Sinha, N., Taylor, J.-S., Kang, C.

(2002) Proc Natl Acad Sci U S A 99: 15965-15970

Released	2003-02-04
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	5'-D(CPGPAPAPTPTPAPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPTPAPAPTPTPCPG)-3' (nucleic acid)

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1SM5 \| pdb_00001sm5	Download File View File

Crystal Structure of a DNA Decamer Containing a Thymine-dimer

Park, H., Zhang, K., Ren, Y., Nadji, S., Sinha, N., Taylor, J.-S., Kang, C.

(2002) Proc Natl Acad Sci U S A 99: 15965-15970

Released	2004-05-25
Method	X-RAY DIFFRACTION 2 Å
Macromolecule	5'-D(CPGPAPAPTPTPAPAPGPC)-3' (nucleic acid) 5'-D(GPCP(BRU)PTPAPAPTP(BRU)PCPG)-3' (nucleic acid)

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1T4I \| pdb_00001t4i	Download File View File

Crystal Structure of a DNA Decamer Containing a Thymine-dimer

Park, H., Zhang, K., Ren, Y., Nadji, S., Sinha, N., Taylor, J.S., Kang, C.

(2002) Proc Natl Acad Sci U S A 99: 15965-15970

Released	2004-05-25
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	5'-D(CPGPAPAPTPTPAPAPGPC)-3' (nucleic acid) 5'-D(GPCPTPTPAPAPTPTPCPG)-3' (nucleic acid)

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3ETU \| pdb_00003etu	Download File View File

Crystal structure of yeast Dsl1p

Ren, Y., Jeffrey, P.D., Hughson, F.M.

(2009) Nat Struct Mol Biol 16: 114-123

Released	2009-01-20
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein transport protein DSL1 (protein)

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3ETV \| pdb_00003etv	Download File View File

Crystal structure of a Tip20p-Dsl1p fusion protein

Ren, Y., Jeffrey, P.D., Hughson, F.M.

(2009) Nat Struct Mol Biol 16: 114-123

Released	2009-01-20
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein transport protein TIP20, Protein transport protein DSL1 chimera (protein)

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3FHN \| pdb_00003fhn	Download File View File

Structure of Tip20p

Tripathi, A., Ren, Y., Jeffrey, P.D., Hughson, F.M.

(2009) Nat Struct Mol Biol 16: 114-123

Released	2009-01-20
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Protein transport protein TIP20 (protein)

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3IKI \| pdb_00003iki	Download File View File

5-SMe-dU containing DNA octamer

Sheng, J., Hassan, A.E.A., Zhang, W., Gan, J., Huang, Z.

(2012) Nucleic Acids Res 40: 8111-8118

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.38 Å
Macromolecule	5'-D(GP(UMS)PGP(US2)PAPCPAPC)-3' (nucleic acid)
Unique Ligands	MG

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3J7V \| pdb_00003j7v	Download File View File

Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions

Guo, F., Liu, Z., Fang, P.A., Zhang, Q., Wright, E.T., Wu, W., Zhang, C., Vago, F., Ren, Y., Jakata, J., Chiu, W., Serwer, P., Jiang, W.

(2014) Proc Natl Acad Sci U S A 111: E4606-E4614

Released	2014-10-15
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Escherichia phage T7
Macromolecule	Major capsid protein 10A (protein)

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3J7W \| pdb_00003j7w	Download File View File

Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions

Guo, F., Liu, Z., Fang, P.A., Zhang, Q., Wright, E.T., Wu, W., Zhang, C., Vago, F., Ren, Y., Jakata, J., Chiu, W., Serwer, P., Jiang, W.

(2014) Proc Natl Acad Sci U S A 111: E4606-E4614

Released	2014-10-15
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Escherichia phage T7
Macromolecule	Major capsid protein 10A (protein)

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3J7X \| pdb_00003j7x	Download File View File

Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions

Guo, F., Liu, Z., Fang, P.A., Zhang, Q., Wright, E.T., Wu, W., Zhang, C., Vago, F., Ren, Y., Jakata, J., Chiu, W., Serwer, P., Jiang, W.

(2014) Proc Natl Acad Sci U S A 111: E4606-E4614

Released	2014-10-15
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Escherichia phage T7
Macromolecule	Major capsid protein 10A (protein)

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3K8P \| pdb_00003k8p	Download File View File

Structural basis for vesicle tethering by the Dsl1 complex

Ren, Y., Jeffrey, P.D., Hughson, F.M.

(2009) Cell 139: 1119-1129

Released	2009-11-10
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Kluyveromyces lactis Saccharomyces cerevisiae
Macromolecule	Dsl1 (protein) Protein transport protein SEC39 (protein)

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3LTR \| pdb_00003ltr	Download File View File

5-OMe-dU containing DNA 8mer

Sheng, J., Hassan, A.E.A., Zhang, W., Gan, J., Huang, Z.

(2012) Nucleic Acids Res 40: 8111-8118

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.3 Å
Macromolecule	5'-D(GP(UMS)PGP(T5O)PAPCPAPC)-3' (nucleic acid)
Unique Ligands	MG

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3MMY \| pdb_00003mmy	Download File View File

Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1

Hoelz, A., Ren, Y.

(2010) Proc Natl Acad Sci U S A 107: 10406-10411

Released	2010-06-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup98 (protein) mRNA export factor (protein)
Unique Ligands	MES

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4K7F \| pdb_00004k7f	Download File View File

Newly identified epitope V60 from HBV core protein complexed with HLA-A*0201

Meng, S.D., Zhang, Y., Wu, Y., Qi, J.X.

(2013) J Virol 87: 8075-8084

Released	2013-06-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Hepatitis B virus Homo sapiens
Macromolecule	Beta-2-microglobulin (protein) Core protein (protein) HLA class I histocompatibility antigen, A-2 alpha chain (protein)

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4L07 \| pdb_00004l07	Download File View File

Crystal structure of the maleamate amidase Ami from Pseudomonas putida S16

Chen, D.D., Lu, Y., Zhang, Z., Wu, G., Xu, P.

(2014) Mol Microbiol 91: 1009-1021

Released	2014-07-16
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Pseudomonas putida S16
Macromolecule	Hydrolase, isochorismatase family (protein)
Unique Ligands	GOL, SO4

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4L08 \| pdb_00004l08	Download File View File

Crystal structure of the maleamate amidase Ami(C149A) in complex with maleate from Pseudomonas putida S16

Chen, D.D., Lu, Y., Zhang, Z., Wu, G., Xu, P.

(2014) Mol Microbiol 91: 1009-1021

Released	2014-07-16
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Pseudomonas putida S16
Macromolecule	Hydrolase, isochorismatase family (protein)
Unique Ligands	MAE

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4N4G \| pdb_00004n4g	Download File View File

Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha

Li, Y., Ren, Y., Li, H.

(2014) Nature 508: 263-268

Released	2014-03-05
Method	X-RAY DIFFRACTION 1.947 Å
Organisms	Mus musculus
Macromolecule	Zinc finger MYND domain-containing protein 11 (protein)
Unique Ligands	PO4, ZN

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4N4H \| pdb_00004n4h	Download File View File

Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.1K36me3

Li, Y., Ren, Y., Li, H.

(2014) Nature 508: 263-268

Released	2014-03-05
Method	X-RAY DIFFRACTION 2.302 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Peptide from Histone H3.1 (protein) Zinc finger MYND domain-containing protein 11 (protein)
Unique Ligands	PEG, PO4, ZN

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4N4I \| pdb_00004n4i	Download File View File

Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3

Li, Y., Ren, Y., Li, H.

(2014) Nature 508: 263-268

Released	2014-03-05
Method	X-RAY DIFFRACTION 1.999 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Peptide from Histone H3.3 (protein) Zinc finger MYND domain-containing protein 11 (protein)
Unique Ligands	PEG, PO4, ZN

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4OWR \| pdb_00004owr	Download File View File

Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair Rae1-Nup98

Ren, Y., Quan, B., Seo, H.S., Blobel, G.

(2014) Proc Natl Acad Sci U S A 111: 9127-9132

Released	2014-06-25
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Homo sapiens Vesicular stomatitis Indiana virus (strain 85CLB South America)
Macromolecule	Matrix protein (protein) Nuclear pore complex protein Nup98-Nup96 (protein) mRNA export factor (protein)

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4TMP \| pdb_00004tmp	Download File View File

Crystal structure of AF9 YEATS bound to H3K9ac peptide

Li, H., Li, Y., Wang, H., Ren, Y.

(2014) Cell 159: 558-571

Released	2014-11-05
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR (protein) Protein AF-9 (protein)
Unique Ligands	EDO

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4TZ4 \| pdb_00004tz4	Download File View File

Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide

Chamberlain, P.P., Pagarigan, B., Delker, S., Leon, B., Riley, M.

To be published

Released	2014-08-06
Method	X-RAY DIFFRACTION 3.01 Å
Organisms	Homo sapiens
Macromolecule	DNA damage-binding protein 1 (protein) Protein cereblon (protein)
Unique Ligands	LVY, ZN