BMRB Entry 11508

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11508
MolProbity Validation Chart

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Title:
Solution structure of the SH2 domain of Csk in complex with a phosphopeptide from Cbp
Deposition date:
2012-09-10
Original release date:
2013-04-08
Authors:
Tanaka, Hiroaki; Akagi, Ken-ichi; Oneyama, Chitose; Tanaka, Masakazu; Sasaki, Yuichi; Kanou, Takashi; Lee, Young-Ho; Yokogawa, Daisuke; Debenecker, Marc-Werner; Nakagawa, Atsushi; Okada, Masato; Ikegami, Takahisa
Citation:

Citation: Tanaka, Hiroaki; Akagi, Ken-ichi; Oneyama, Chitose; Tanaka, Masakazu; Sasaki, Yuichi; Kanou, Takashi; Lee, Young-Ho; Yokogawa, Daisuke; Debenecker, Marc-Werner; Nakagawa, Atsushi; Okada, Masato; Ikegami, Takahisa. "A new SH2 domain binding mode of C-terminal Src kianse to Cbp/PAG""  .

Assembly members:

Assembly members:
Csk_SH2, polymer, 99 residues, 11473.218 Da.
Cbp_phosphopeptide, polymer, 38 residues, 4263.602 Da.

Natural source:

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukayota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-6p-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Csk_SH2: GPLGSMPWFHGKITREQAER LLYPPETGLFLVRESTNYPG DYTLCVSCEGKVEHYRIMYH ASKLSIDEEVYFENLMQLVE HYTTDADGLCTRLIKPKVM
Cbp_phosphopeptide: GPLGSKRFSSLSYKSREEDP TLTEEEISAMXSSVNKPG

Data sets:
Data typeCount
13C chemical shifts581
15N chemical shifts137
1H chemical shifts887

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 99 residues - 11473.218 Da.

Residues 1-5 represent a non native affinity tag

1   GLYPROLEUGLYSERMETPROTRPPHEHIS
2   GLYLYSILETHRARGGLUGLNALAGLUARG
3   LEULEUTYRPROPROGLUTHRGLYLEUPHE
4   LEUVALARGGLUSERTHRASNTYRPROGLY
5   ASPTYRTHRLEUCYSVALSERCYSGLUGLY
6   LYSVALGLUHISTYRARGILEMETTYRHIS
7   ALASERLYSLEUSERILEASPGLUGLUVAL
8   TYRPHEGLUASNLEUMETGLNLEUVALGLU
9   HISTYRTHRTHRASPALAASPGLYLEUCYS
10   THRARGLEUILELYSPROLYSVALMET

Entity 2, entity_2 38 residues - 4263.602 Da.

Residues 1-5 represent a non-native affinity tag

1   GLYPROLEUGLYSERLYSARGPHESERSER
2   LEUSERTYRLYSSERARGGLUGLUASPPRO
3   THRLEUTHRGLUGLUGLUILESERALAMET
4   PTRSERSERVALASNLYSPROGLY

Samples:

sample_1: Csk SH2 domain, [U-13C; U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Cbp phosphopeptide0.5 – 1.0 mM; H2O 90%; D2O, [U-99% 2H], 10%

sample_2: Csk SH2 domain, [U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Cbp phosphopeptide0.5 – 1.0 mM; H2O 90%; D2O, [U-99% 2H], 10%

sample_3: Cbp phosphopeptide, [U-13C; U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Csk SH2 domain0.5 – 1.0 mM; H2O 90%; D2O, [U-99% 2H], 10%

sample_4: Cbp phosphopeptide, [U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Csk SH2 domain0.5 – 1.0 mM; H2O 90%; D2O, [U-99% 2H], 10%

sample_5: Csk SH2 domain, [U-13C; U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Cbp phosphopeptide0.5 – 1.0 mM; D2O, [U-99% 2H], 100%

sample_6: Cbp phosphopeptide, [U-13C; U-15N], 0.5 – 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; Csk SH2 domain0.5 – 1.0 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0.076 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_5isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_6isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_5isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_6isotropicsample_conditions_1
2D DQF-COSYsample_5isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_3isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_6isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESYsample_5isotropicsample_conditions_1
3D 1H-13C NOESYsample_6isotropicsample_conditions_1
2D CBHDsample_5isotropicsample_conditions_1
2D CBHDsample_6isotropicsample_conditions_1
2D CBHEsample_5isotropicsample_conditions_1
2D CBHEsample_6isotropicsample_conditions_1
3D 13C-filtered/13C-edited NOESYsample_5isotropicsample_conditions_1
3D 13C-filtered/13C-edited NOESYsample_6isotropicsample_conditions_1
3D 13C,15N-filtered/15N-edited NOESYsample_3isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

Molmol, Koradi, Billeter and Wuthrich - geometry optimization

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker DRX 800 MHz

Related Database Links:

UNP P32577 Q9JM80
PDB
DBJ BAE23297 BAE33565 BAE42047 BAG60052 BAA95413 BAC30545 BAC40842 BAE33539 BAE42829
EMBL CAA41484
GB AAA18766 AAH18394 AAH52006 AAH98863 AAX90624 AAG44565 AAI45329 AAI45762 AAI45764 EDL05179
PRF 1709363A
REF NP_001025210 NP_001291690 NP_031809 XP_003463668 XP_004628790 NP_001181960 NP_071589 NP_444412 XP_005066844 XP_006530170
SP P32577 P41241 Q3U1F9 Q9JM80
AlphaFold Q4G003 P32577 P41241 Q9JM80 Q3U1F9 Q9JM80

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks