3C5N

Structure of human TULP1 in complex with IP3

• PDB DOI: https://doi.org/10.2210/pdb3C5N/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-01-31 Released: 2008-04-01 
• Deposition Author(s): Busam, R.D., Lehtio, L., Arrowsmith, C.H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Weigelt, J., Welin, M., Berglund, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Structure of human TULP1 in complex with IP3

Busam, R.D., Lehtio, L., Arrowsmith, C.H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Weigelt, J., Welin, M., Berglund, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.31 kDa 
• Atom Count: 3,994 
• Modelled Residue Count: 454 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubby-related protein 1	A, B	246	Homo sapiens	Mutation(s): 0  Gene Names: TULP1, TUBL1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O00294 (Homo sapiens) Explore O00294  Go to UniProtKB:  O00294
PHAROS:  O00294 GTEx:  ENSG00000112041

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3P	C [auth A], D [auth B], E [auth B]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C6 H15 O15 P3 MMWCIQZXVOZEGG-XJTPDSDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.31	α = 90
b = 83.63	β = 94.01
c = 57.68	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Busam, R.D., Lehtio, L., Arrowsmith, C.H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Weigelt, J., Welin, M., Berglund, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations