PDB-5oo6: Complex of human nuclear cap-binding complex with ARS2 C-terminal...

ID or keywords:

Entry

Database: PDB / ID: 5oo6

Title

Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide

Components

Nuclear cap-binding protein subunit 1
Nuclear cap-binding protein subunit 2
Serrate RNA effector molecule homolog

Keywords

NUCLEAR PROTEIN / Complex nuclear cap-binding complex m7GTP C-terminal peptide from ARS2

Function / homology

Function and homology information

mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs ...mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs /

snRNA binding / positive regulation of RNA binding /

RNA cap binding / alternative mRNA splicing, via spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / neuronal stem cell population maintenance /

regulation of mRNA processing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / : / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / mRNA 3'-end processing / response to arsenic-containing substance / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of translational initiation / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of neurogenesis / Signaling by FGFR2 IIIa TM / spliceosomal complex assembly / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 7-methylguanosine mRNA capping / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Formation of HIV-1 elongation complex containing HIV-1 Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway /

RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II /

mRNA splicing, via spliceosome /

mRNA processing / Regulation of expression of SLITs and ROBOs / protein-macromolecule adaptor activity /

snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity /

nuclear body /

ribonucleoprotein complex /

mRNA binding / regulation of DNA-templated transcription / protein-containing complex /

mitochondrion /

DNA binding /

RNA binding /

nucleoplasm /

nucleus /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Cusack, S. / Schulze, W.M.

Citation

Journal: Nat Commun / Year: 2017
Title: Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2.
Authors: Schulze, W.M. / Cusack, S.

History

Deposition	Aug 6, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5oo6.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb5oo6.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5oo6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oo/5oo6 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/5oo6	HTTPS FTP

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Related structure data

Related structure data	5oobC 1h2tS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oob-1 5oob-2 1n52-d 5t2b-d 5oob-4 6d0y-d 6mum-1 2wxn-d 4xe0-d 4tv3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5oobC

1h2tS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (10) #230 - Feb 2019 Initiation Factor eIF4E similarity (8) #205 - Jan 2017 Nuclear Pore Complex similarity (5) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (4) #67 - Jul 2005 TATA-Binding Protein similarity (2) #60 - Dec 2004 Ubiquitin similarity (2) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (2) #130 - Oct 2010 Riboswitches similarity (1) #65 - May 2005 Self-splicing RNA similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#245 - May 2020
Spliceosomes
similarity (10)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (8)
#205 - Jan 2017
Nuclear Pore Complex
similarity (5)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (4)
#67 - Jul 2005
TATA-Binding Protein
similarity (2)
#60 - Dec 2004
Ubiquitin
similarity (2)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (2)
#234 - Jun 2019
MDM2 and Cancer
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)

Deposited unit

A: Nuclear cap-binding protein subunit 1

B: Nuclear cap-binding protein subunit 2

D: Nuclear cap-binding protein subunit 1

E: Nuclear cap-binding protein subunit 2

G: Nuclear cap-binding protein subunit 1

H: Nuclear cap-binding protein subunit 2

J: Nuclear cap-binding protein subunit 1

K: Nuclear cap-binding protein subunit 2

M: Nuclear cap-binding protein subunit 1

N: Nuclear cap-binding protein subunit 2

P: Nuclear cap-binding protein subunit 1

Q: Nuclear cap-binding protein subunit 2

S: Nuclear cap-binding protein subunit 1

T: Nuclear cap-binding protein subunit 2

V: Nuclear cap-binding protein subunit 1

W: Nuclear cap-binding protein subunit 2

C: Serrate RNA effector molecule homolog

F: Serrate RNA effector molecule homolog

I: Serrate RNA effector molecule homolog

L: Serrate RNA effector molecule homolog

O: Serrate RNA effector molecule homolog

R: Serrate RNA effector molecule homolog

U: Serrate RNA effector molecule homolog

X: Serrate RNA effector molecule homolog

hetero molecules

911 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nuclear cap-binding protein subunit 1

B: Nuclear cap-binding protein subunit 2

C: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
Evidence: gel filtration
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Nuclear cap-binding protein subunit 1

E: Nuclear cap-binding protein subunit 2

F: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Nuclear cap-binding protein subunit 1

H: Nuclear cap-binding protein subunit 2

I: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Nuclear cap-binding protein subunit 1

K: Nuclear cap-binding protein subunit 2

L: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: Nuclear cap-binding protein subunit 1

N: Nuclear cap-binding protein subunit 2

O: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

P: Nuclear cap-binding protein subunit 1

Q: Nuclear cap-binding protein subunit 2

R: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

S: Nuclear cap-binding protein subunit 1

T: Nuclear cap-binding protein subunit 2

U: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

V: Nuclear cap-binding protein subunit 1

W: Nuclear cap-binding protein subunit 2

X: Serrate RNA effector molecule homolog

hetero molecules

defined by author&software
114 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.520, 112.990, 270.980
Angle α, β, γ (deg.)	90.00, 90.30, 90.02
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	1	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
1	2	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	2	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
1	3	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	3	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
1	4	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	4	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
1	5	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	5	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
1	6	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	6	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	7	THR	THR	ALA	ALA	A	A	27 - 790	9 - 772
2	7	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	8	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	8	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
1	9	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	9	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
1	10	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	10	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
1	11	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	11	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
1	12	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	12	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
1	13	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	13	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	14	GLY	GLY	LYS	LYS	B	B	4 - 151	6 - 153
2	14	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	15	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	15	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
1	16	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	16	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
1	17	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	17	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
1	18	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	18	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
1	19	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	19	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	20	THR	THR	ALA	ALA	D	C	27 - 790	9 - 772
2	20	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	21	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	21	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
1	22	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	22	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
1	23	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	23	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
1	24	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	24	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
1	25	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	25	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	26	GLY	GLY	LYS	LYS	E	D	4 - 151	6 - 153
2	26	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	27	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
2	27	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
1	28	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
2	28	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
1	29	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
2	29	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
1	30	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
2	30	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	31	THR	THR	ALA	ALA	G	E	27 - 790	9 - 772
2	31	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	32	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
2	32	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
1	33	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
2	33	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
1	34	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
2	34	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
1	35	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
2	35	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	36	GLY	GLY	LYS	LYS	H	F	4 - 151	6 - 153
2	36	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	37	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
2	37	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
1	38	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
2	38	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
1	39	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
2	39	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	40	THR	THR	ALA	ALA	J	G	27 - 790	9 - 772
2	40	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	41	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
2	41	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
1	42	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
2	42	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
1	43	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
2	43	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	44	GLY	GLY	LYS	LYS	K	H	4 - 151	6 - 153
2	44	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	45	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
2	45	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
1	46	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
2	46	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	47	THR	THR	ALA	ALA	M	I	27 - 790	9 - 772
2	47	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	48	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
2	48	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
1	49	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
2	49	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	50	GLY	GLY	LYS	LYS	N	J	4 - 151	6 - 153
2	50	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	51	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
2	51	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
1	52	THR	THR	ALA	ALA	P	K	27 - 790	9 - 772
2	52	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	53	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
2	53	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
1	54	GLY	GLY	LYS	LYS	Q	L	4 - 151	6 - 153
2	54	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	55	THR	THR	ALA	ALA	S	M	27 - 790	9 - 772
2	55	THR	THR	ALA	ALA	V	O	27 - 790	9 - 772
1	56	GLY	GLY	LYS	LYS	T	N	4 - 151	6 - 153
2	56	GLY	GLY	LYS	LYS	W	P	4 - 151	6 - 153
1	57	ASP	ASP	PHE	PHE	C	Q	852 - 871	29 - 48
2	57	ASP	ASP	PHE	PHE	F	R	852 - 871	29 - 48
1	58	ASP	ASP	PHE	PHE	C	Q	852 - 871	29 - 48
2	58	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
1	59	ASP	ASP	PHE	PHE	C	Q	852 - 871	29 - 48
2	59	ASP	ASP	PHE	PHE	O	U	852 - 871	29 - 48
1	60	ASP	ASP	PHE	PHE	C	Q	852 - 871	29 - 48
2	60	ASP	ASP	PHE	PHE	R	V	852 - 871	29 - 48
1	61	ASP	ASP	PHE	PHE	C	Q	852 - 871	29 - 48
2	61	ASP	ASP	PHE	PHE	X	X	852 - 871	29 - 48
1	62	ASP	ASP	PHE	PHE	F	R	852 - 871	29 - 48
2	62	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
1	63	ASP	ASP	PHE	PHE	F	R	852 - 871	29 - 48
2	63	ASP	ASP	PHE	PHE	O	U	852 - 871	29 - 48
1	64	ASP	ASP	PHE	PHE	F	R	852 - 871	29 - 48
2	64	ASP	ASP	PHE	PHE	R	V	852 - 871	29 - 48
1	65	ASP	ASP	PHE	PHE	F	R	852 - 871	29 - 48
2	65	ASP	ASP	PHE	PHE	X	X	852 - 871	29 - 48
1	66	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
2	66	ASP	ASP	PHE	PHE	L	T	852 - 871	29 - 48
1	67	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
2	67	ASP	ASP	PHE	PHE	O	U	852 - 871	29 - 48
1	68	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
2	68	ASP	ASP	PHE	PHE	R	V	852 - 871	29 - 48
1	69	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
2	69	ASP	ASP	PHE	PHE	U	W	852 - 871	29 - 48
1	70	ASP	ASP	PHE	PHE	I	S	852 - 871	29 - 48
2	70	ASP	ASP	PHE	PHE	X	X	852 - 871	29 - 48
1	71	ASP	ASP	PHE	PHE	L	T	852 - 871	29 - 48
2	71	ASP	ASP	PHE	PHE	U	W	852 - 871	29 - 48
1	72	ASP	ASP	PHE	PHE	O	U	852 - 871	29 - 48
2	72	ASP	ASP	PHE	PHE	R	V	852 - 871	29 - 48
1	73	ASP	ASP	PHE	PHE	O	U	852 - 871	29 - 48
2	73	ASP	ASP	PHE	PHE	X	X	852 - 871	29 - 48
1	74	ASP	ASP	PHE	PHE	R	V	852 - 871	29 - 48
2	74	ASP	ASP	PHE	PHE	X	X	852 - 871	29 - 48

NCS ensembles :

#1: Protein	Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit Mass: 89809.984 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: CBP80 delta NLS Extra N-terminal methonine Mutation A479V Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP1, CBP80, NCBP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09161
#2: Protein	Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1 Mass: 18156.260 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Additional GA at N-terminus after TEV cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Production host: Escherichia coli (E. coli) / References: UniProt: P52298
#3: Protein/peptide	Serrate RNA effector molecule homolog / Arsenite-resistance protein 2 Mass: 5384.940 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Additional GAM at N-terminus after TEV cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXP5
#4: Chemical	ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE Mass: 539.223 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₁H₂₀N₅O₁₄P₃

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was ...Details: CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.

Crystal

Density Matthews: 2.39 Å³/Da / Density % sol: 48.56 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.8→280 Å / Num. obs: 200837 / % possible obs: 97.5 % / Redundancy: 2.08 % / CC_1/2: 0.995 / R_sym value: 0.097 / Net I/σ(I): 6.63
Reflection shell	Resolution: 2.8→2.91 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 21706 / CC_1/2: 0.585 / R_sym value: 0.697 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1H2T

1h2t

Resolution: 2.8→270.98 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.899 / SU B: 22.713 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26798	10059	5 %	RANDOM
R_work	0.23051	-	-	-
obs	0.23236	190778	97.48 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 71.494 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5 Å²	-0.17 Å²	0.38 Å²
2-	-	-4.78 Å²	0.05 Å²
3-	-	-	-0.23 Å²

Refinement step

Cycle: 1 / Resolution: 2.8→270.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	58479	0	264	0	58743

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	60140
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	55603
X-RAY DIFFRACTION	r_angle_refined_deg	1.194	1.961	81402
X-RAY DIFFRACTION	r_angle_other_deg	0.893	3	129084
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.399	5	7084
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.677	23.896	2949
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.095	15	10745
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.14	15	403
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	8875
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	65613
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	12534
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.167	7.201	28489
X-RAY DIFFRACTION	r_mcbond_other	3.167	7.201	28488
X-RAY DIFFRACTION	r_mcangle_it	5.25	10.788	35519
X-RAY DIFFRACTION	r_mcangle_other	5.25	10.788	35520
X-RAY DIFFRACTION	r_scbond_it	2.891	7.379	31651
X-RAY DIFFRACTION	r_scbond_other	2.891	7.379	31651
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.943	10.951	45883
X-RAY DIFFRACTION	r_long_range_B_refined	7.587	81.47	66858
X-RAY DIFFRACTION	r_long_range_B_other	7.587	81.468	66858
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	49538	0.01
1	2	D	49538	0.01
2	1	A	49580	0.02
2	2	G	49580	0.02
3	1	A	49616	0.01
3	2	J	49616	0.01
4	1	A	49536	0.01
4	2	M	49536	0.01
5	1	A	49648	0.01
5	2	P	49648	0.01
6	1	A	49604	0.01
6	2	S	49604	0.01
7	1	A	49778	0
7	2	V	49778	0
8	1	B	9318	0
8	2	E	9318	0
9	1	B	9314	0
9	2	H	9314	0
10	1	B	9320	0
10	2	K	9320	0
11	1	B	9318	0
11	2	N	9318	0
12	1	B	9322	0
12	2	Q	9322	0
13	1	B	9318	0
13	2	T	9318	0
14	1	B	9326	0
14	2	W	9326	0
15	1	D	49698	0.02
15	2	G	49698	0.02
16	1	D	49798	0.01
16	2	J	49798	0.01
17	1	D	50472	0.01
17	2	M	50472	0.01
18	1	D	49758	0.01
18	2	P	49758	0.01
19	1	D	49606	0.01
19	2	S	49606	0.01
20	1	D	49540	0.01
20	2	V	49540	0.01
21	1	E	9320	0
21	2	H	9320	0
22	1	E	9318	0
22	2	K	9318	0
23	1	E	9338	0
23	2	N	9338	0
24	1	E	9324	0
24	2	Q	9324	0
25	1	E	9318	0
25	2	T	9318	0
26	1	E	9310	0
26	2	W	9310	0
27	1	G	49724	0.02
27	2	J	49724	0.02
28	1	G	49682	0.02
28	2	M	49682	0.02
29	1	G	49874	0.02
29	2	P	49874	0.02
30	1	G	49504	0.02
30	2	S	49504	0.02
31	1	G	49582	0.02
31	2	V	49582	0.02
32	1	H	9312	0
32	2	K	9312	0
33	1	H	9322	0
33	2	N	9322	0
34	1	H	9330	0
34	2	Q	9330	0
35	1	H	9310	0
35	2	T	9310	0
36	1	H	9312	0
36	2	W	9312	0
37	1	J	49788	0.01
37	2	M	49788	0.01
38	1	J	49798	0.01
38	2	P	49798	0.01
39	1	J	49710	0
39	2	S	49710	0
40	1	J	49620	0.01
40	2	V	49620	0.01
41	1	K	9310	0
41	2	N	9310	0
42	1	K	9318	0
42	2	Q	9318	0
43	1	K	9336	0
43	2	T	9336	0
44	1	K	9316	0
44	2	W	9316	0
45	1	M	49752	0.01
45	2	P	49752	0.01
46	1	M	49586	0.01
46	2	S	49586	0.01
47	1	M	49538	0.01
47	2	V	49538	0.01
48	1	N	9326	0
48	2	Q	9326	0
49	1	N	9310	0
49	2	T	9310	0
50	1	N	9310	0
50	2	W	9310	0
51	1	P	49566	0.01
51	2	S	49566	0.01
52	1	P	49648	0.01
52	2	V	49648	0.01
53	1	Q	9320	0
53	2	T	9320	0
54	1	Q	9316	0
54	2	W	9316	0
55	1	S	49608	0.01
55	2	V	49608	0.01
56	1	T	9318	0
56	2	W	9318	0
57	1	C	596	0.1
57	2	F	596	0.1
58	1	C	548	0.07
58	2	I	548	0.07
59	1	C	596	0.1
59	2	O	596	0.1
60	1	C	598	0.11
60	2	R	598	0.11
61	1	C	608	0.05
61	2	X	608	0.05
62	1	F	548	0
62	2	I	548	0
63	1	F	610	0
63	2	O	610	0
64	1	F	606	0
64	2	R	606	0
65	1	F	596	0.08
65	2	X	596	0.08
66	1	I	462	0.05
66	2	L	462	0.05
67	1	I	548	0
67	2	O	548	0
68	1	I	548	0
68	2	R	548	0
69	1	I	464	0.01
69	2	U	464	0.01
70	1	I	548	0.05
70	2	X	548	0.05
71	1	L	464	0.05
71	2	U	464	0.05
72	1	O	606	0
72	2	R	606	0
73	1	O	596	0.08
73	2	X	596	0.08
74	1	R	598	0.1
74	2	X	598	0.1

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	674	-
R_work	0.386	13958	-
obs	-	-	96.17 %

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