RCSB PDB: Search

2L2K \| pdb_00002l2k	Download File View File

Solution NMR structure of the R/G STEM LOOP RNA-ADAR2 DSRBM2 Complex

Allain, F.H.-T., Oberstrass, F.C., Stefl, R.

(2010) Cell 143: 225-237

Released	2010-10-27
Method	SOLUTION NMR
Organisms	Homo sapiens Mus musculus
Macromolecule	Adenosine deaminase (protein) RNA (42-MER) (nucleic acid)

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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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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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5ED1 \| pdb_00005ed1	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from S. cerevisiae BDF2 gene

Matthews, M.M., Fisher, A.J., Beal, P.A.

(2016) Nat Struct Mol Biol 23: 426-433

Released	2016-04-13
Method	X-RAY DIFFRACTION 2.77 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5'-R(GPAPCPUPGPAPAPCPGPAPCPCPAPAPUPGPUPGPGPGPGPAPA)-3') (nucleic acid) RNA (5'-R(UPUPCPCPCPCPAPCPAPUPUP(8AZ)PGPAPCPGPUPUPCPAPGPUPC)-3') (nucleic acid)
Unique Ligands	IHP, ZN

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5ED2 \| pdb_00005ed2	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene

Matthews, M.M., Fisher, A.J.

(2016) Nat Struct Mol Biol 23: 426-433

Released	2016-04-13
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5'-R(PCPAPGPAPGPCPCPCPCPCPCPAPGPCPAPUPCPGPCPGPAPGPC)-3') (nucleic acid) RNA (5'-R(PGPCPUPCPGPCPGPAPUPGPCPUP(8AZ)PGPAPGPGPGPCPUPCPUPG)-3') (nucleic acid)
Unique Ligands	IHP, ZN

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5HP2 \| pdb_00005hp2	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA sequence derived from S. cerevisiae BDF2 gene with AU basepair at reaction site

Matthews, M.M., Fisher, A.J., Beal, P.A.

(2016) Nat Struct Mol Biol 23: 426-433

Released	2016-04-13
Method	X-RAY DIFFRACTION 2.983 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5'-R(GPAPCPUPGPAPAPCPGPAPCPUPAPAPUPGPUPGPGPGPGPAPA)-3') (nucleic acid) RNA (5'-R(UPUPCPCPCPCPAPCPAPUPUP(8AZ)PGPAPCPGPUPUPCPAPGPUPC)-3') (nucleic acid)
Unique Ligands	IHP, ZN

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5HP3 \| pdb_00005hp3	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA sequence derived from S. cerevisiae BDF2 gene with AC mismatch at reaction site

Matthews, M.M., Fisher, A.J., Beal, P.A.

(2016) Nat Struct Mol Biol 23: 426-433

Released	2016-04-13
Method	X-RAY DIFFRACTION 3.091 Å
Organisms	Homo sapiens Saccharomyces cerevisiae
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5'-R(GPAPCPUPGPAPAPCPGPAPCPCPAPAPUPGPUPGPGPGPGPAPA)-3') (nucleic acid) RNA (5'-R(UPUPCPCPCPCPAPCPAPUPUP(8AZ)PGPAPCPGPUPUPCPAPGPUPC)-3') (nucleic acid)
Unique Ligands	IHP, ZN

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6D06 \| pdb_00006d06	Download File View File

Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base

Matthews, M.M., Fisher, A.J., Beal, P.A.

(2019) Cell Chem Biol 26: 269

Released	2019-02-20
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5'-R(CPAPGPAPGPCPCPCPCPCPNPAPGPCPAPUPCPGPCPGPAPGPC)-3') (nucleic acid) RNA (5'-R(GPCPUPCPGPCPGPAPUPGPCPUP(8AZ)PGPAPGPGPGPCPUPCPUPG)-3') (nucleic acid)
Unique Ligands	IHP, ZN

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6VFF \| pdb_00006vff	Download File View File

Dimer of Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene

Thuy-boun, A.S., Fisher, A.J., Beal, P.A.

(2020) Nucleic Acids Res 48: 7958-7972

Released	2020-07-01
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5-R(GPCPUPCPGPCPGPAPUPGPCPUP(8AZ)PGPAPGPGPGPCP UPCPUPGPAPUPAPGPCPUPAPCPG)-3) (nucleic acid) RNA(5-R(CPGPUPAPGPCPUPAPUPCPAPGPAPGPCPCPCPCPCPCPAPGPCPAPUPCPGPCPGPAPGPC)-3) (nucleic acid)
Unique Ligands	IHP, ZN

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7F60 \| pdb_00007f60	Download File View File

Crystal structure of auxiliary protein in complex with human nuclear protein

Gao, X., Cui, S.

(2022) Nat Commun 13: 4782

Released	2022-09-14
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Nuclear pore complex protein Nup98-Nup96 (protein) ORF6 protein (protein) mRNA export factor (protein)

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7F90 \| pdb_00007f90	Download File View File

Crystal structure of SARS auxiliary protein in complex with human nuclear protein

Gao, X., Cui, S.

(2022) Nat Commun 13: 4782

Released	2022-09-14
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	Nuclear pore complex protein Nup98-Nup96 (protein) ORF6 protein (protein) mRNA export factor (protein)

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7KFN \| pdb_00007kfn	Download File View File

Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing a 2'-deoxy Benner's Base Z opposite the edited base

Wilcox, X.E., Fisher, A.J., Beal, P.A.

(2021) J Am Chem Soc 143: 6865-6876

Released	2021-06-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) Gli1 1W5 23mer RNA (nucleic acid) Gli1 8AZ 23mer RNA (nucleic acid)
Unique Ligands	IHP, ZN

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7MNI \| pdb_00007mni	Download File View File

Crystal structure of the N-terminal domain of NUP88 in complex with NUP98 C-terminal Autoproteolytic Domain

Bley, C.J., Nie, S., Mobbs, G.W., Petrovic, S., Gres, A.T., Liu, X., Mukherjee, S., Harvey, S., Huber, F.M., Lin, D.H., Brown, B., Tang, A.W., Rundlet, E.J., Correia, A.R., Chen, S., Regmi, S.G., Stevens, T.A., Jette, C.A., Dasso, M., Patke, A., Palazzo, A.F., Kossiakoff, A.A., Hoelz, A.

(2022) Science 376: eabm9129-eabm9129

Released	2022-06-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup88 (protein) Nuclear pore complex protein Nup98 (protein)

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7Q64 \| pdb_00007q64	Download File View File

Cryo-em structure of the Nup98 fibril polymorph 1

Ibanez de Opakua, A., Geraets, J.A., Frieg, B., Dienemann, C., Savastano, A., Rankovic, M., Cima-Omori, M.-S., Schroeder, G.F., Zweckstetter, M.

(2022) Nat Chem 14: 1278-1285

Released	2022-10-12
Method	ELECTRON MICROSCOPY 2.76 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup98 (protein)

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7Q65 \| pdb_00007q65	Download File View File

Cryo-em structure of the Nup98 fibril polymorph 2

Ibanez de Opakua, A., Geraets, J.A., Frieg, B., Dienemann, C., Savastano, A., Rankovic, M., Cima-Omori, M.-S., Schroeder, G.F., Zweckstetter, M.

(2022) Nat Chem 14: 1278-1285

Released	2022-10-12
Method	ELECTRON MICROSCOPY 3.32 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup98 (protein)

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7Q66 \| pdb_00007q66	Download File View File

Cryo-em structure of the Nup98 fibril polymorph 3

Ibanez de Opakua, A., Geraets, J.A., Frieg, B., Dienemann, C., Savastano, A., Rankovic, M., Cima-Omori, M.-S., Schroeder, G.F., Zweckstetter, M.

(2022) Nat Chem 14: 1278-1285

Released	2022-10-12
Method	ELECTRON MICROSCOPY 2.79 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup98 (protein)

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7Q67 \| pdb_00007q67	Download File View File

Cryo-em structure of the Nup98 fibril polymorph 4

Ibanez de Opakua, A., Geraets, J.A., Frieg, B., Dienemann, C., Savastano, A., Rankovic, M., Cima-Omori, M.-S., Schroeder, G.F., Zweckstetter, M.

(2022) Nat Chem 14: 1278-1285

Released	2022-10-12
Method	ELECTRON MICROSCOPY 3.37 Å
Organisms	Homo sapiens
Macromolecule	Nuclear pore complex protein Nup98 (protein)

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7VPG \| pdb_00007vpg	Download File View File

Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98

Li, T., Guo, H., Yang, T., Wen, Y., Ji, X.

(2021) Front Mol Biosci 8: 813248-813248

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 (protein) ORF6 protein (protein) mRNA export factor (protein)

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7VPH \| pdb_00007vph	Download File View File

Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98

Li, T., Guo, H., Yang, T., Wen, Y., Ji, X.

(2021) Front Mol Biosci 8: 813248-813248

Released	2022-01-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 (protein) ORF6 protein (protein) mRNA export factor (protein)

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8E0F \| pdb_00008e0f	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing a G-G pair adjacent to the target site

Wilcox, X.E., Fisher, A.J., Beal, P.A.

(2022) Nucleic Acids Res 50: 10857-10868

Released	2022-10-26
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5-R(GPCPUPCPGPCPGPAPUPGPCPGP(8AZ)PGPAPGPGPGPCP UPCPUPGPAPUPAPGPCPUPAPCPG)-3) (nucleic acid) RNA(5-R(CPGPUPAPGPCPUPAPUPCPAPGPAPGPCPCPCPCPCPCPGPGPCPAPUPCPGPCPGPAPGPC)-3) (nucleic acid)
Unique Ligands	IHP, ZN

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8E4X \| pdb_00008e4x	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2-R2D) bound to dsRNA containing a G:3-deaza dA pair adjacent to the target site

Fisher, A.J., Mendoza, H.G.

(2022) Nucleic Acids Res 50: 10857-10868

Released	2022-10-26
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Double-stranded RNA-specific editase 1 (protein) RNA (5-R(GPCPUPCPGPCPGPAPUPGPCPGP(8AZ)PGPAPGPGPGPCP UPCPUPGPAPUPAPGPCPUPAPCPG)-3) (nucleic acid) RNA(5-R(CPGPUPAPGPCPUPAPUPCPAPGPAPGPCPCPCPCPCPCP(4DU)GPCPAPUPCPGPCPGPAPGPC)-3) (nucleic acid)
Unique Ligands	IHP, ZN

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9D5J \| pdb_00009d5j	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing deoxyinosine at the -1 position of the guide strand

Fisher, A.J., Cheng, J., Manjunath, A., Campbell, K.

(2024) Biomolecules 14:

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Isoform 4 of Double-stranded RNA-specific editase 1 (protein) RNA Top Strand Containing 8-azanebularine (8AZ) (nucleic acid) RNA Bottom Strand containing deoxyinosine complementary to a guanosine adjacent to the target site (hybrid)
Unique Ligands	EDO, IHP, ZN

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9D5K \| pdb_00009d5k	Download File View File

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing an expanded cytidine analog at the -1 position of the guide strand

Fisher, A.J., Cheng, J., Manjunath, A., Campbell, K.

(2024) Biomolecules 14:

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.697 Å
Organisms	Homo sapiens
Macromolecule	Isoform 4 of Double-stranded RNA-specific editase 1 (protein) RNA Top Strand (nucleic acid) RNA Bottom Strand (hybrid)
Unique Ligands	IHP, MG, ZN

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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

2L2K | pdb_00002l2k

3MMY | pdb_00003mmy

4OWR | pdb_00004owr

5ED1 | pdb_00005ed1

5ED2 | pdb_00005ed2

5HP2 | pdb_00005hp2

5HP3 | pdb_00005hp3

6D06 | pdb_00006d06

6VFF | pdb_00006vff

7F60 | pdb_00007f60

7F90 | pdb_00007f90

7KFN | pdb_00007kfn

7MNI | pdb_00007mni

7Q64 | pdb_00007q64

7Q65 | pdb_00007q65

7Q66 | pdb_00007q66

7Q67 | pdb_00007q67

7VPG | pdb_00007vpg

7VPH | pdb_00007vph

8E0F | pdb_00008e0f

8E4X | pdb_00008e4x

9D5J | pdb_00009d5j

9D5K | pdb_00009d5k