BMRBj - BMREntryMaster

Found 1 Document (1.003 seconds)

BMRB: 16194

2KG1

Structure of the third 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. third qRRM of hnRNP F (polymer, Thiol state: all free), 105 monomers, 11496.58 Da Detail

GDSEFTVQST TGHCVHMRGL PYKATENDIY NFFSPLNPVR VHIEIGPDGR VTGEADVEFA THEEAVAAMS KDRANMQHRY IELFLNSTTG ASNGAYSSQV MQGMG

Total weight

13514.79 Da

Max. entity weight

11496.58 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.4 %, Completeness (bb): 79.8 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.4 % (1014 of 1245)	93.0 % (596 of 641)	63.2 % (309 of 489)	94.8 % (109 of 115)
Backbone	79.8 % (549 of 688)	97.2 % (245 of 252)	60.6 % (203 of 335)	100.0 % (101 of 101)
Sidechain	85.0 % (554 of 652)	90.2 % (351 of 389)	78.3 % (195 of 249)	57.1 % (8 of 14)
Aromatic	66.4 % (85 of 128)	92.2 % (59 of 64)	43.3 % (26 of 60)	0.0 % (0 of 4)
Methyl	96.9 % (95 of 98)	98.0 % (48 of 49)	95.9 % (47 of 49)

1. AGGGAU G-tract RNA

AGGGAU

2. third qRRM of hnRNP F

GDSEFTVQST TGHCVHMRGL PYKATENDIY NFFSPLNPVR VHIEIGPDGR VTGEADVEFA THEEAVAAMS KDRANMQHRY IELFLNSTTG ASNGAYSSQV MQGMG

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 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	4.0 ppm	internal	indirect	0.0
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.0

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.0 ppm	internal	indirect	0.0
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.0

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.0 ppm	internal	indirect	0.0
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	4.7 ppm	internal	indirect	0.0

Referencing offset: 0.11 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KG1, 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

Related entities 2. third qRRM of hnRNP F, : 1 : 7 : 61 entities Detail

Interaction partners 2. third 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_16194_2kg1.nef
Input source #2: Coordindates	2kg1.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

-----250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----350-------360-------370-------380-
AAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGMG
|||||||||||||||||||||||||||||||||||||||
AAMSKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGMG
-------110-------120-------130---------

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	139	0	0	100.0
B	B	6	0	0	100.0

Content subtype: combined_16194_2kg1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	999		75.5 (chain: A, length: 139), 100.0 (chain: B, length: 6)
1	Distance restraints	AMBER_distance_constraints_2	OK	1542 (1)	noe	72.7 (chain: A, length: 139), 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: 139, Sequence coverage: 75.5%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 602
  - ¹⁵N chemical shifts: 114
  - ¹³C chemical shifts: 283
- 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	771	550	71.3
¹⁵N chemical shifts	153	114	74.5
¹³C chemical shifts	581	283	48.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	211	72.8
¹⁵N chemical shifts	134	101	75.4
¹³C chemical shifts	278	89	32.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	481	339	70.5
¹⁵N chemical shifts	19	13	68.4
¹³C chemical shifts	303	194	64.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	51	79.7
¹³C chemical shifts	64	50	78.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	47	72.3
¹³C chemical shifts	65	26	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	48	98.0
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	36	100.0
¹³C chemical shifts	30	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3
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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 139, Sequence coverage: 72.7%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of restraints: 1541
- Weight of restraints: 1.0 (1541)
- Potential type of restraints: square-well-parabolic (1541)
- Range of distance target values: 2.35, 4.86 (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 (1.003 seconds)

BMRB: 16194

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 2. third qRRM of hnRNP F, : 1 : 7 : 61 entities Detail

Interaction partners 2. third 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