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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yildirim, I."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (20)
	synthetic construct (9)
	Aequorea victoria (3)
	Mus musculus (3)

Taxonomy

	Eukaryota (20)
	other sequences (9)

Experimental Method

	ELECTRON MICROSCOPY (15)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

	DNA (20)
	Protein (20)

Refinement Resolution (Å)

	2.5 - 3.0 (3)
	3.0 - 3.5 (7)
	3.5 - 4.0 (3)
	4.0 - 4.5 (3)
	> 4.5 (4)

Release Date

	2015 - 2019 (12)
	2020 - 2024 (8)

Enzyme Classification Name

Transferases (3)

Symmetry Type

	Asymmetric (17)
	Cyclic (3)

AllSelected

1 to 20 of 20 Structures

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5EF6 \| pdb_00005ef6	Download File View File

Structure of HOXB13 complex with methylated DNA

Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

(2017) Science 356:

Released	2017-02-08
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Homeobox protein Hox-B13 (protein) DNA (5'-D(PGPGPAPCPCPTP(5CM)PGPTPAPAPAPAPCPAPCPAPA)-3') (nucleic acid) DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM)PGPAPGPGPTPCPC)-3') (nucleic acid)

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5EGO \| pdb_00005ego	Download File View File

HOXB13-MEIS1 heterodimer bound to methylated DNA

Morgunova, E., Yin, Y., Jolma, A., Popov, A., Taipale, J.

(2017) Science 356:

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Homeobox protein Hox-B13 (protein) Homeobox protein Meis1 (protein) DNA (5'-D(CPCPTP(5CM)PGPTPAPAPAPAPCPTPGPTPCPAPAPC)-3') (nucleic acid) DNA (5'-D(PGPTPTPGPAPCPAPGPTPTPTPTPAP(5CM)PGPAPGPG)-3') (nucleic acid)

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5HOD \| pdb_00005hod	Download File View File

Structure of LHX4 transcription factor complexed with DNA

Morgunova, E., Yin, Y., Popov, A., Taipale, J.

(2017) Science 356:

Released	2017-02-01
Method	X-RAY DIFFRACTION 2.682 Å
Organisms	Homo sapiens
Macromolecule	LIM/homeobox protein Lhx4 (protein) DNA (5'-D(PAPCPCPTPAPAPTPTPAPGPGPCPGPTPAPAPTPTPAPG)-3') (nucleic acid) DNA (5'-D(PCPTPAPAPTPTPAPCPGPCPCPTPAPAPTPTPAPGPGPT)-3') (nucleic acid)

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5LTY \| pdb_00005lty	Download File View File

Homeobox transcription factor CDX2 bound to methylated DNA

Morgunova, E., Popov, A., Taipale, J.

(2017) Science 356:

Released	2017-05-31
Method	X-RAY DIFFRACTION 2.66 Å
Organisms	Homo sapiens
Macromolecule	Homeobox protein CDX-2 (protein) DNA (5'-D(PGPGPAPGPGPTP(5CM)PGPTPAPAPAPAPCPAPCPAPA)-3') (nucleic acid) DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM)PGPAPCPCPTPCPC)-3') (nucleic acid)

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5LUX \| pdb_00005lux	Download File View File

Homeobox transcription factor CDX1 bound to methylated DNA

Morgunova, E., Popov, A., Taipale, J.

(2017) Science 356:

Released	2017-05-17
Method	X-RAY DIFFRACTION 3.23 Å
Organisms	Homo sapiens
Macromolecule	Homeobox protein CDX-1 (protein) DNA (5'-D(PGPAPGPGPTP(5CM)PGPTPAPAPAPAPCPAPCPAPA)-3') (nucleic acid) DNA (5'-D(PGPGPAPGPGPTP(5CM)PGPTPAPAPAPAPCPAPCPAPA)-3') (nucleic acid) DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM)PGPAPCPCPTPC)-3') (nucleic acid) DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM)PGPAPCPCPTPCPC)-3') (nucleic acid)

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6R8Y \| pdb_00006r8y	Download File View File

Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 4.3 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2

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6R8Z \| pdb_00006r8z	Download File View File

Cryo-EM structure of NCP_THF2(-1)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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6R90 \| pdb_00006r90	Download File View File

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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6R91 \| pdb_00006r91	Download File View File

Cryo-EM structure of NCP_THF2(-3)-UV-DDB

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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6R92 \| pdb_00006r92	Download File View File

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 4.8 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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6R93 \| pdb_00006r93	Download File View File

Cryo-EM structure of NCP-6-4PP

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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6R94 \| pdb_00006r94	Download File View File

Cryo-EM structure of NCP_THF2(-3)

Matsumoto, S., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2019) Nature 571: 79-84

Released	2019-06-12
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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6T90 \| pdb_00006t90	Download File View File

OCT4-SOX2-bound nucleosome - SHL-6

Michael, A.K., Kempf, G., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2020) Science 368: 1460-1465

Released	2020-05-06
Method	ELECTRON MICROSCOPY 3.05 Å
Organisms	Aequorea victoria Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	PTD

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6T93 \| pdb_00006t93	Download File View File

Nucleosome with OCT4-SOX2 motif at SHL-6

Michael, A.K., Kempf, G., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2020) Science 368: 1460-1465

Released	2020-05-06
Method	ELECTRON MICROSCOPY 3.49 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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6YOV \| pdb_00006yov	Download File View File

OCT4-SOX2-bound nucleosome - SHL+6

Michael, A.K., Kempf, G., Cavadini, S., Bunker, R.D., Thoma, N.H.

(2020) Science 368: 1460-1465

Released	2020-05-06
Method	ELECTRON MICROSCOPY 3.42 Å
Organisms	Aequorea victoria Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 8 Unique nucleic acid chains: 1
Unique Ligands	PTD

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8OSJ \| pdb_00008osj	Download File View File

Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1)

Michael, A.K., Stoos, L., Kempf, G., Cavadini, S., Thoma, N.H.

(2023) Nature 619: 385-393

Released	2023-05-24
Method	ELECTRON MICROSCOPY 6.2 Å
Organisms	Homo sapiens Mus musculus synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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8OSK \| pdb_00008osk	Download File View File

Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map)

Stoos, L., Michael, A.K., Kempf, G., Cavadini, S., Thoma, N.H.

(2023) Nature 619: 385-393

Released	2023-05-24
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Homo sapiens Mus musculus synthetic construct
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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8OSL \| pdb_00008osl	Download File View File

Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement)

Michael, A.K., Stoos, L., Kempf, G., Cavadini, S., Thoma, N.

(2023) Nature 619: 385-393

Released	2023-05-24
Method	ELECTRON MICROSCOPY 4.9 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Unique protein chains: 6 Unique nucleic acid chains: 2

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8OTS \| pdb_00008ots	Download File View File

OCT4 and MYC-MAX co-bound to a nucleosome

Michael, A.K., Stoos, L., Kempf, G., Cavadini, S., Thoma, N.

(2023) Nature 619: 385-393

Released	2023-05-24
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Aequorea victoria Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	PTD

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8OTT \| pdb_00008ott	Download File View File

MYC-MAX bound to a nucleosome at SHL+5.8

Stoos, L., Michael, A.K., Kempf, G., Kater, L., Cavadini, S., Thoma, N.

(2023) Nature 619: 385-393

Released	2023-05-24
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 2
Unique Ligands	PTD

1 to 20 of 20 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

5EF6 | pdb_00005ef6

Structure of HOXB13 complex with methylated DNA

5EGO | pdb_00005ego

HOXB13-MEIS1 heterodimer bound to methylated DNA

5HOD | pdb_00005hod

Structure of LHX4 transcription factor complexed with DNA

5LTY | pdb_00005lty

Homeobox transcription factor CDX2 bound to methylated DNA

5LUX | pdb_00005lux

Homeobox transcription factor CDX1 bound to methylated DNA

6R8Y | pdb_00006r8y

Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

6R8Z | pdb_00006r8z

Cryo-EM structure of NCP_THF2(-1)-UV-DDB

6R90 | pdb_00006r90

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

6R91 | pdb_00006r91

Cryo-EM structure of NCP_THF2(-3)-UV-DDB

6R92 | pdb_00006r92

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B

6R93 | pdb_00006r93

Cryo-EM structure of NCP-6-4PP

6R94 | pdb_00006r94

Cryo-EM structure of NCP_THF2(-3)

6T90 | pdb_00006t90

OCT4-SOX2-bound nucleosome - SHL-6

6T93 | pdb_00006t93

Nucleosome with OCT4-SOX2 motif at SHL-6

6YOV | pdb_00006yov

OCT4-SOX2-bound nucleosome - SHL+6

8OSJ | pdb_00008osj

Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1)

8OSK | pdb_00008osk

Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map)

8OSL | pdb_00008osl

Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement)

8OTS | pdb_00008ots

OCT4 and MYC-MAX co-bound to a nucleosome

8OTT | pdb_00008ott

MYC-MAX bound to a nucleosome at SHL+5.8

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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

5EF6 | pdb_00005ef6

5EGO | pdb_00005ego

5HOD | pdb_00005hod

5LTY | pdb_00005lty

5LUX | pdb_00005lux

6R8Y | pdb_00006r8y

6R8Z | pdb_00006r8z

6R90 | pdb_00006r90

6R91 | pdb_00006r91

6R92 | pdb_00006r92

6R93 | pdb_00006r93

6R94 | pdb_00006r94

6T90 | pdb_00006t90

6T93 | pdb_00006t93

6YOV | pdb_00006yov

8OSJ | pdb_00008osj

8OSK | pdb_00008osk

8OSL | pdb_00008osl

8OTS | pdb_00008ots

8OTT | pdb_00008ott