BMRBj - BMREntryMaster

Found 1 Document (0.756 seconds)

BMRB: 15543

2JX2

Solution conformation of RNA-bound NELF-E RRM

Authors

Jampani, N., Schweimer, K., Wenzel, S., Woehrl, B.M., Roesch, P.

Assembly

rna bound nelfe-rrm

Entity

1. rna bound nelfe-rrm (polymer, Thiol state: all free), 121 monomers, 13362.92 Da Detail

MGSSHHHHHH SSGLVPRGSH MGPFRRSDSF PERRAPRKGN TLYVYGEDMT PTLLRGAFSP FGNIIDLSMD PPRNCAFVTY EKMESADQAV AELNGTQVES VQLKVNIARK QPMLDAATGK S

2. TAR(49-57) (polymer, Thiol state: not available), 9 monomers, 2957.779 Da Detail

UAGGGAACC

Total weight

16320.699 Da

Max. entity weight

13362.92 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 72.3 %, Completeness: 50.0 %, Completeness (bb): 50.1 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	50.0 % (753 of 1506)	54.1 % (428 of 791)	39.7 % (234 of 590)	72.8 % (91 of 125)
Backbone	50.1 % (404 of 807)	55.9 % (166 of 297)	38.9 % (155 of 398)	74.1 % (83 of 112)
Sidechain	52.1 % (422 of 810)	53.2 % (263 of 494)	49.8 % (151 of 303)	61.5 % (8 of 13)
Aromatic	12.9 % (18 of 140)	22.9 % (16 of 70)	3.0 % (2 of 66)	0.0 % (0 of 4)
Methyl	91.2 % (93 of 102)	90.2 % (46 of 51)	92.2 % (47 of 51)

1. rna bound nelfe-rrm

MGSSHHHHHH SSGLVPRGSH MGPFRRSDSF PERRAPRKGN TLYVYGEDMT PTLLRGAFSP FGNIIDLSMD PPRNCAFVTY EKMESADQAV AELNGTQVES VQLKVNIARK QPMLDAATGK S

2. TAR(49-57)

UAGGGAACC

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	rna bound nelfe-rrm	[U-98% 13C; U-98% 15N]		0.4 mM
2	TAR(49-57)	natural abundance		0.8 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JX2, Strand ID: A Detail

Release date

2008-11-02

Citation

NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding
Jampani, N., Schweimer, K., Wenzel, S., Woehrl, B.M., Roesch, P.
Biochemistry (2008), 47, 3756-3761, PubMed 18303858 , DOI 10.1021/bi702429m , Abstract

Related entities 1. rna bound nelfe-rrm, : 1 : 1 : 12 : 27 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15543_2jx2.nef
Input source #2: Coordindates	2jx2.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MGSSHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVES
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVES

-------110-------120-
VQLKVNIARKQPMLDAATGKS
|||||||||||||||||||||
VQLKVNIARKQPMLDAATGKS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0

Content subtype: combined_15543_2jx2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	727		76.0 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2099 (1)	noe	67.8 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	48 (1)	hbond	28.1 (chain: A, length: 121)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	32 (32)	.	36.4 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 76.0%
- Total number of assignments
  - ¹H chemical shifts: 412
  - ¹⁵N chemical shifts: 91
  - ¹³C chemical shifts: 224
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	714	412	57.7
¹⁵N chemical shifts	130	91	70.0
¹³C chemical shifts	530	224	42.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	243	166	68.3
¹⁵N chemical shifts	112	83	74.1
¹³C chemical shifts	242	77	31.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	471	246	52.2
¹⁵N chemical shifts	18	8	44.4
¹³C chemical shifts	288	147	51.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	49	86.0
¹³C chemical shifts	57	49	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	12	23.5
¹³C chemical shifts	51	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 67.8%
- Total number of restraints: 2099
- Weight of restraints: 1.0 (2099)
- Potential type of restraints: square-well-parabolic (2099)
- Range of distance target values: 1.5, 3.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 28.1%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: square-well-parabolic (48)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 36.4%
- Total number of restraints: 32
- Total number of restraints per polymer type: 32
- Weight of restraints: 1.0 (32)
- Potential type of restraints: square-well-parabolic (32)
- Dihedral angle restraints per residue

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 (0.756 seconds)

BMRB: 15543

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. rna bound nelfe-rrm, : 1 : 1 : 12 : 27 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail