BMRB Entry 31138

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31138
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
HADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin
Deposition date:
2024-01-15
Original release date:
2024-05-17
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, 194 residues, 22238.340 Da.
entity_2, polymer, 58 residues, 6431.449 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: EDSDIAFLIDGSGSIIPHDF RRMKEFVSTVMEQLKKSKTL FSLMQYSEEFRIHFTFKEFQ NNPNPRSLVKPITQLLGRTH TATGIRKVVRELFNITNGAR KNAFKILVVITDGEKFGDPL GYEDVIPEADREGVIRYVIG VGDAFRSEKSRQELNTIASK PPRDHVFQVNNFEALKTIQN QLREKIFAIEGTQT
entity_2: GKKEKPEKKVKKSDCGEWQW SVCVPTSGDCGLGTREGTRT GAECKQTMKTQRCKIPCN

Data sets:
Data typeCount
13C chemical shifts891
15N chemical shifts224
1H chemical shifts1111

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 194 residues - 22238.340 Da.

1   GLUASPSERASPILEALAPHELEUILEASP
2   GLYSERGLYSERILEILEPROHISASPPHE
3   ARGARGMETLYSGLUPHEVALSERTHRVAL
4   METGLUGLNLEULYSLYSSERLYSTHRLEU
5   PHESERLEUMETGLNTYRSERGLUGLUPHE
6   ARGILEHISPHETHRPHELYSGLUPHEGLN
7   ASNASNPROASNPROARGSERLEUVALLYS
8   PROILETHRGLNLEULEUGLYARGTHRHIS
9   THRALATHRGLYILEARGLYSVALVALARG
10   GLULEUPHEASNILETHRASNGLYALAARG
11   LYSASNALAPHELYSILELEUVALVALILE
12   THRASPGLYGLULYSPHEGLYASPPROLEU
13   GLYTYRGLUASPVALILEPROGLUALAASP
14   ARGGLUGLYVALILEARGTYRVALILEGLY
15   VALGLYASPALAPHEARGSERGLULYSSER
16   ARGGLNGLULEUASNTHRILEALASERLYS
17   PROPROARGASPHISVALPHEGLNVALASN
18   ASNPHEGLUALALEULYSTHRILEGLNASN
19   GLNLEUARGGLULYSILEPHEALAILEGLU
20   GLYTHRGLNTHR

Entity 2, unit_2 58 residues - 6431.449 Da.

1   GLYLYSLYSGLULYSPROGLULYSLYSVAL
2   LYSLYSSERASPCYSGLYGLUTRPGLNTRP
3   SERVALCYSVALPROTHRSERGLYASPCYS
4   GLYLEUGLYTHRARGGLUGLYTHRARGTHR
5   GLYALAGLUCYSLYSGLNTHRMETLYSTHR
6   GLNARGCYSLYSILEPROCYSASN

Samples:

sample_1: human alphaM I-domain, [U-13C; U-15N], 0.2 mM; The N-terminal domain of pleiotrophin 1 mM

sample_2: human alphaM I-domain, [U-13C; U-15N], 0.5 mM

sample_3: The N-terminal domain of pleiotrophin, [U-13C; U-15N], 0.5 mM

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

Experiments:

NameSampleSample stateSample conditions
3D F1-13C-edited/F3-13C,15N-filtered HSQCNOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_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