BMRB Entry 36619

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36619
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
NMR structure of p75NTR juxtamembrane domain in complex with RhoGDI N-terminal domain containing a phosphorylation-mimicking S34D mutation
Deposition date:
2023-11-28
Original release date:
2026-02-06
Authors:
Lin, Z.; Li, Z.
Citation:

Citation: Ramanujan, Ajeena; Li, Zhen; Ma, Yanchen; Lin, Zhi; Ibanez, Carlos. "RhoGDI phosphorylation by PKC promotes its interaction with death receptor p75(NTR) to gate axon growth and neuron survival."  EMBO Rep. 25, 1490-1512 (2024).
PubMed: 38253689

Assembly members:

Assembly members:
Rho GDP-dissociation inhibitor 1, polymer, 61 residues, 6875.394 Da.
Tumor necrosis factor receptor superfamily member 16, polymer, 62 residues, 6661.135 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: not available   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rho GDP-dissociation inhibitor 1: GSAEQEPTAEQLAQIAAENE EDEHSVNYKPPAQKDIQEIQ ELDKDDESLRKYKEALLGRV A
Tumor necrosis factor receptor superfamily member 16: GSKRWNSCKQNKQGANSRPV NQTPPPEGEKLHSDSGISVD SQSLHDQQPHTQTASGQALK GD

Data sets:
Data typeCount
13C chemical shifts339
15N chemical shifts117
1H chemical shifts684

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 61 residues - 6875.394 Da.

1   GLYSERALAGLUGLNGLUPROTHRALAGLU
2   GLNLEUALAGLNILEALAALAGLUASNGLU
3   GLUASPGLUHISSERVALASNTYRLYSPRO
4   PROALAGLNLYSASPILEGLNGLUILEGLN
5   GLULEUASPLYSASPASPGLUSERLEUARG
6   LYSTYRLYSGLUALALEULEUGLYARGVAL
7   ALA

Entity 2, entity_2 62 residues - 6661.135 Da.

1   GLYSERLYSARGTRPASNSERCYSLYSGLN
2   ASNLYSGLNGLYALAASNSERARGPROVAL
3   ASNGLNTHRPROPROPROGLUGLYGLULYS
4   LEUHISSERASPSERGLYILESERVALASP
5   SERGLNSERLEUHISASPGLNGLNPROHIS
6   THRGLNTHRALASERGLYGLNALALEULYS
7   GLYASP

Samples:

sample_1: RhoGDI-NTD, [U-13C; U-15N], 0.8 mM; p75NTR-JMD 2.4 mM; PIPES 10 mM; H2O 90.0%; D2O, [U-2H], 10.0%

sample_2: RhoGDI-NTD 2.4 mM; p75NTR-JMD, [U-13C; U-15N], 0.8 mM; PIPES 10 mM; H2O 90.0%; D2O, [U-2H], 10.0%

sample_conditions_1: ionic strength: 10 mM; pH: 6.8; pressure: 1 Pa; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1anisotropicsample_conditions_1
2D 1H-13C HSQCsample_1anisotropicsample_conditions_1
3D CBCA(CO)NHsample_1anisotropicsample_conditions_1
3D HNCACBsample_1anisotropicsample_conditions_1
3D H(CCCO)NHsample_1anisotropicsample_conditions_1
3D CC(CO)NHsample_1anisotropicsample_conditions_1
3D HCCH-TOCSYsample_1anisotropicsample_conditions_1
3D 13C,13C-NOESYsample_1anisotropicsample_conditions_1
3D 15N,13C-NOESYsample_1anisotropicsample_conditions_1
3D 13C,15N-filtered NOESYsample_1anisotropicsample_conditions_1
2D 1H-15N HSQCsample_2anisotropicsample_conditions_1
3D HCCH-TOCSYsample_2anisotropicsample_conditions_1
3D CBCA(CO)NHsample_2anisotropicsample_conditions_1
3D HNCACBsample_2anisotropicsample_conditions_1
3D H(CCCO)NHsample_2anisotropicsample_conditions_1
3D CC(CO)NHsample_2anisotropicsample_conditions_1
3D 13C,13C-NOESYsample_2anisotropicsample_conditions_1
3D 15N,13C-NOESYsample_2anisotropicsample_conditions_1
3D 13C,15N-filtered NOESYsample_2anisotropicsample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMRView, Johnson, One Moon Scientific - data analysis

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

NMR spectrometers:

  • Bruker AVANCE 800 MHz

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