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BMRB: 25854

2N8L

Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC

Authors

Nicastro, G., Candel, A.M., Ramos, A., Hollingworth, D.

Assembly

Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC

Entity

1. Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC, entity 1 (polymer, Thiol state: not present), 191 monomers, 20657.36 Da Detail

GAMGPSSVSG AAPFSSFMPP EQETVHVFIP AQAVGAIIGK KGQHIKQLSR FASASIKIAP PETPDSKVRM VVITGPPEAQ FKAQGRIYGK LKEENFFGPK EEVKLETHIR VPASAAGRVI GDDGKTVNEL QNLTAAEVVV PRDQTPDENE QVIVKIIGHF YASQMAQRKI RDILAQVKQQ HQKGQSGQLQ A

2. Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC, entity 2 (polymer, Thiol state: not present), 7 monomers, 2202.335 Da Detail

CACACCC

Total weight

22859.695 Da

Max. entity weight

20657.36 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.3 %, Completeness: 60.4 %, Completeness (bb): 55.7 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C
All	60.4 % (1282 of 2124)	66.0 % (808 of 1225)	52.7 % (474 of 899)
Backbone	55.7 % (567 of 1018)	60.8 % (259 of 426)	52.0 % (308 of 592)
Sidechain	66.0 % (846 of 1281)	68.7 % (549 of 799)	61.6 % (297 of 482)
Aromatic	22.2 % (32 of 144)	44.4 % (32 of 72)	0.0 % (0 of 72)
Methyl	84.8 % (178 of 210)	86.7 % (91 of 105)	82.9 % (87 of 105)

1. entity 1

2. entity 2

CACACCC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 20mM phosphate buffer and 20mM of NaCl at pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.3 mM
2	entity_2	natural abundance	0.3 mM
3	phosphate buffer	natural abundance	20 mM
4	potassium phosphate	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291
³¹P	DSS	methyl protons	na	indirect	0.4048086

Referencing offset: -0.06 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 12 models in PDB: 2N8L, Strand ID: A Detail

Release date

2015-10-22

Citation 1

ZBP1 recognition of beta-actin zipcode induces RNA looping
Chao, J.A., Patskovsky, Y., Patel, V., Levy, M., Almo, S.C., Singer, R.H.
Genes. Dev. (2010), 24, 148-158, PubMed 20080952 , DOI 10.1101/gad.1862910 , Abstract

Show more 2 citaions

Citation 2

Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control
Patel, V.L., Mitra, S., Harris, R., Buxbaum, A.R., Lionnet, T., Brenowitz, M., Girvin, M., Levy, M., Almo, S.C., Singer, R.H., Chao, J.A.
Genes. Dev. (2012), 26, 43-53, PubMed 22215810 , DOI 10.1101/gad.177428.111 , Abstract

Citation 3

KH domains with impaired nucleic acid binding as a tool for functional analysis
Hollingworth, D., Candel, A.M., Nicastro, G., Martin, S.R., Briata, P., Gherzi, R., Ramos, A.
Nucleic Acids Res. (2012), 40, 6873-6886, PubMed 22547390 , DOI 10.1093/nar/gks368 , Abstract

Hide non-primary 2 citaions

Entries sharing articles BMRB: 2, Swiss-Prot: 3 entries Detail

  BMRB: 25855 released on 2015-10-22
    Title Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU
  BMRB: 17815 released on 2012-04-22
    Title Backbone 1H, 13C and 15N resonance assignments for IMP1 KH34
  Swiss-Prot: O00425 released on 2007-04-03
    Title IF2B3_HUMAN Entity Insulin-like growth factor 2 mRNA-binding protein 3
  Swiss-Prot: Q9NZI8 released on 2007-04-03
    Title IF2B1_HUMAN Entity Insulin-like growth factor 2 mRNA-binding protein 1
  Swiss-Prot: Q9Y6M1 released on 2006-06-27
    Title IF2B2_HUMAN Entity Insulin-like growth factor 2 mRNA-binding protein 2

Related entities 1. Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC, entity 1, : 1 : 2 : 94 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25854_2n8l.nef
Input source #2: Coordindates	2n8l.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
GAMGPSSVSGAAPFSSFMPPEQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVVITGPPEAQFKAQGRIYGKLKEENFFGPK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGPSSVSGAAPFSSFMPPEQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVVITGPPEAQFKAQGRIYGKLKEENFFGPK

-------110-------120-------130-------140-------150-------160-------170-------180-------190-
EEVKLETHIRVPASAAGRVIGDDGKTVNELQNLTAAEVVVPRDQTPDENEQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQKGQSGQLQA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EEVKLETHIRVPASAAGRVIGDDGKTVNELQNLTAAEVVVPRDQTPDENEQVIVKIIGHFYASQMAQRKIRDILAQVKQQHQKGQSGQLQA

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

--------
GCACACCC
||||||||
GCACACCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	191	0	0	100.0
B	B	8	0	0	100.0

Content subtype: combined_25854_2n8l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1154		79.1 (chain: A, length: 191)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2499 (1)	noe	80.6 (chain: A, length: 191), 100.0 (chain: B, length: 8)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	8 (1)	hbond	25.0 (chain: B, length: 8)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 79.1%
- Total number of assignments
  - ¹H chemical shifts: 751
  - ¹³C chemical shifts: 403
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	1159	751	64.8
¹³C chemical shifts	850	403	47.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	384	221	57.6
¹³C chemical shifts	382	128	33.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	775	530	68.4
¹³C chemical shifts	468	275	58.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	95	87.2
¹³C chemical shifts	109	87	79.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	28	48.3
¹³C chemical shifts	58	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: 191, Sequence coverage: 80.6%
  - Entity_assembly_ID: B, Chain length: 8, Sequence coverage: 100.0%
- Total number of restraints: 2499
- Weight of restraints: 1.0 (2499)
- Potential type of restraints: square-well-parabolic (2499)
- Range of distance target values: 1.65, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 8, Sequence coverage: 25.0%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Range of distance target values: 1.7, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords KH Domain, NMR Solution Structure, RNA Binding Protein

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Found 1 Document (0.953 seconds)

BMRB: 25854

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2, Swiss-Prot: 3 entries Detail

Related entities 1. Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target CACACCC, entity 1, : 1 : 2 : 94 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail