BMRBj - BMREntryMaster

Found 1 Document (1.106 seconds)

BMRB: 16193

2KG0

Structure of the second qRRM domain of hnRNP F in complex with a AGGGAU G-tract RNA

Authors

Allain, F.H.T., Dominguez, C.

Assembly

hnRNP F/AGGGAU G-tract RNA complex

Entity

1. AGGGAU G-tract RNA (polymer, Thiol state: not present), 6 monomers, 2018.210 Da Detail

AGGGAU

2. second qRRM of hnRNP F (polymer, Thiol state: not present), 92 monomers, 10215.35 Da Detail

NSADSANDGF VRLRGLPFGC TKEEIVQFFS GLEIVPNGIT LPVDPEGKIT GEAFVQFASQ ELAEKALGKH KERIGHRYIE VFKSSQEEVR SY

Total weight

12233.56 Da

Max. entity weight

10215.35 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 89.2 %, Completeness (bb): 88.5 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.2 % (1039 of 1165)	95.9 % (584 of 609)	79.4 % (363 of 457)	92.9 % (92 of 99)
Backbone	88.5 % (540 of 610)	95.1 % (214 of 225)	80.8 % (240 of 297)	97.7 % (86 of 88)
Sidechain	90.3 % (576 of 638)	96.4 % (370 of 384)	82.3 % (200 of 243)	54.5 % (6 of 11)
Aromatic	63.3 % (76 of 120)	95.0 % (57 of 60)	33.9 % (19 of 56)	0.0 % (0 of 4)
Methyl	98.9 % (93 of 94)	100.0 % (47 of 47)	97.9 % (46 of 47)

1. AGGGAU G-tract RNA

AGGGAU

2. second qRRM of hnRNP F

NSADSANDGF VRLRGLPFGC TKEEIVQFFS GLEIVPNGIT LPVDPEGKIT GEAFVQFASQ ELAEKALGKH KERIGHRYIE VFKSSQEEVR SY

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 ~ 1.5 mM
2	entity_2	[U-13C; U-15N]	1.0 ~ 1.5 mM
3	NaH2PO4	natural abundance	20 mM
4	NaCl	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.25
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.25
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.25
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	indirect	0.25
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.1

Referencing offset: -0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KG0, Strand ID: A Detail

Release date

2010-06-14

Citation

Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs
Dominguez, C., Fisette, J., Chabot, B., Allain, F.H.T.
Nat. Struct. Mol. Biol. (2010), 17, 853-861, PubMed 20526337 , DOI 10.1038/nsmb.1814 , Abstract

Entries sharing articles BMRB: 2, Swiss-Prot: 1 entries Detail

  BMRB: 16192 released on 2010-06-14
    Title NMR structure of the first qRRM of hnRNP F in complex with AGGGAU G-tract RNA
  BMRB: 16194 released on 2010-06-14
    Title Structure of the third qRRM domain of hnRNP F in complex with a AGGGAU G-tract RNA
  Swiss-Prot: P52597 released on 1996-10-01
    Title HNRPF_HUMAN Entity Heterogeneous nuclear ribonucleoprotein F

Related entities 2. second qRRM of hnRNP F, : 1 : 7 : 1 : 316 entities Detail

Interaction partners 2. second qRRM of hnRNP F, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 4 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16193_2kg0.nef
Input source #2: Coordindates	2kg0.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-70-------80--------90-------100-------110-------120-------130-------140-------150-------160-------1
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

70-------180-------190----
LGKHKERIGHRYIEVFKSSQEEVRSY
||||||||||||||||||||||||||
LGKHKERIGHRYIEVFKSSQEEVRSY
-------110-------120------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------
AGGGAU
||||||
AGGGAU

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	126	0	0	100.0
B	B	6	0	0	100.0

Content subtype: combined_16193_2kg0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1049		72.2 (chain: A, length: 126), 100.0 (chain: B, length: 6)
1	Distance restraints	AMBER_distance_constraints_2	Warning	2911 (1)	noe	69.0 (chain: A, length: 126), 100.0 (chain: B, length: 6)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 72.2%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 595
  - ¹⁵N chemical shifts: 97
  - ¹³C chemical shifts: 357
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	739	541	73.2
¹⁵N chemical shifts	137	97	70.8
¹³C chemical shifts	549	357	65.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	263	182	69.2
¹⁵N chemical shifts	121	86	71.1
¹³C chemical shifts	252	162	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	476	359	75.4
¹⁵N chemical shifts	16	11	68.8
¹³C chemical shifts	297	195	65.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	47	82.5
¹³C chemical shifts	57	46	80.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	46	75.4
¹³C chemical shifts	61	14	23.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	45	91.8
¹⁵N chemical shifts	4	0	0.0
¹³C chemical shifts	39	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	34	94.4
¹³C chemical shifts	30	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	11	84.6
¹⁵N chemical shifts	4	0	0.0
¹³C chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	0	0.0

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 69.0%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of restraints: 2908
- Weight of restraints: 1.0 (2908)
- Potential type of restraints: square-well-parabolic (2908)
- Range of distance target values: 2.35, 5.12 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords G tract, polyadenylation regulation, protein-RNA complex, splicing regulation

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.106 seconds)

BMRB: 16193

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2, Swiss-Prot: 1 entries Detail

Related entities 2. second qRRM of hnRNP F, : 1 : 7 : 1 : 316 entities Detail

Interaction partners 2. second qRRM of hnRNP F, : 1 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail