BMRB Entry 31139

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/BMR31139
MolProbity Validation Chart

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

Title:
HADDOCK models of active human alphaM I-domain bound to the the C-terminal domain of the cytokine pleiotrophin
Deposition date:
2024-01-15
Original release date:
2024-05-15
Authors:
Wang, X.; Nguyen, H.
Citation:

Citation: Wang, X.; Nguyen, H.. "NMR structure of alphaM I-domain of integrin Mac-1 in complex with the Cytokine Pleiotrophin"  .

Assembly members:

Assembly members:
entity_1, polymer, 184 residues, 21148.152 Da.
entity_2, polymer, 57 residues, 6472.498 Da.
entity_MG, non-polymer, 24.305 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DSDIAFLIDGSGSIIPHDFR RMKEFVSTVMEQLKKSKTLF SLMQYSEEFRIHFTFKEFQN NPNPRSLVKPITQLLGRTHT ATGIRKVVRELFNITNGARK NAFKILVVITDGEKFGDPLG YEDVIPEADREGVIRYVIGV GDAFRSEKSRQELNTIASKP PRDHVFQVNNFEALKTIQNQ LREK
entity_2: NWKKQFGAECKYQFQAWGEC DLNTALKTRTGSLKRALHNA ECQKTVTISKPCGKLTK

Data sets:
Data typeCount
13C chemical shifts432
15N chemical shifts129
1H chemical shifts367

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 184 residues - 21148.152 Da.

1   ASPSERASPILEALAPHELEUILEASPGLY
2   SERGLYSERILEILEPROHISASPPHEARG
3   ARGMETLYSGLUPHEVALSERTHRVALMET
4   GLUGLNLEULYSLYSSERLYSTHRLEUPHE
5   SERLEUMETGLNTYRSERGLUGLUPHEARG
6   ILEHISPHETHRPHELYSGLUPHEGLNASN
7   ASNPROASNPROARGSERLEUVALLYSPRO
8   ILETHRGLNLEULEUGLYARGTHRHISTHR
9   ALATHRGLYILEARGLYSVALVALARGGLU
10   LEUPHEASNILETHRASNGLYALAARGLYS
11   ASNALAPHELYSILELEUVALVALILETHR
12   ASPGLYGLULYSPHEGLYASPPROLEUGLY
13   TYRGLUASPVALILEPROGLUALAASPARG
14   GLUGLYVALILEARGTYRVALILEGLYVAL
15   GLYASPALAPHEARGSERGLULYSSERARG
16   GLNGLULEUASNTHRILEALASERLYSPRO
17   PROARGASPHISVALPHEGLNVALASNASN
18   PHEGLUALALEULYSTHRILEGLNASNGLN
19   LEUARGGLULYS

Entity 2, unit_2 57 residues - 6472.498 Da.

1   ASNTRPLYSLYSGLNPHEGLYALAGLUCYS
2   LYSTYRGLNPHEGLNALATRPGLYGLUCYS
3   ASPLEUASNTHRALALEULYSTHRARGTHR
4   GLYSERLEULYSARGALALEUHISASNALA
5   GLUCYSGLNLYSTHRVALTHRILESERLYS
6   PROCYSGLYLYSLEUTHRLYS

Entity 3, unit_3 - Mg - 24.305 Da.

1   MG

Samples:

sample_1: active human alphaM I-domain, [U-100% 13C; U-100% 15N], 0.3 mM

sample_2: The C-terminal Domain of Pleiotrophin, [U-100% 13C; U-100% 15N], 1.0 mM

sample_3: active human alphaM I-domain, [U-100% 13C; U-100% 15N; U-80% 2H], 0.2 mM; The C-terminal Domain of Pleiotrophin 1.0 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
4D 13C-HSQC-NOESY-15N-HMQCsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1

Software:

NMRViewJ, Bruce Johnson - chemical shift assignment

HADDOCK, Bonvin - structure calculation

NMR spectrometers:

  • Bruker AVANCE III HD 850 MHz

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