4D0M

Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3

PDB DOI: https://doi.org/10.2210/pdb4D0M/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-04-29 Released: 2014-05-28
Deposition Author(s): Burke, J.E., Inglis, A.J., Perisic, O., Masson, G.R., McLaughlin, S.H., Rutaganira, F., Shokat, K.M., Williams, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 6.00 Å
R-Value Free: 0.359
R-Value Work: 0.253
R-Value Observed: 0.259

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structures of Pi4Kiiibeta Complexes Show Simultaneous Recruitment of Rab11 and its Effectors.

Burke, J.E., Inglis, A.J., Perisic, O., Masson, G.R., Mclaughlin, S.H., Rutaganira, F., Shokat, K.M., Williams, R.L.

(2014) Science 344: 1035

PubMed: 24876499 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1253397
Primary Citation of Related Structures:
4D0L, 4D0M

PubMed Abstract:
Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases, and their effectors is unknown. Here, we describe structures of PI4Kβ (PI4KIIIβ) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIβ interface is distinct compared with known structures of Rab complexes and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIβ coordinates Rab11 and its effectors on PI4P-enriched membranes and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIβ to combat malaria.

Organizational Affiliation

Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. jeburke@uvic.ca rlw@mrc-lmb.cam.ac.uk.

Macromolecule Content

Total Structure Weight: 1,149.87 kDa
Atom Count: 65,970
Modelled Residue Count: 8,154
Deposited Residue Count: 9,996
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATIDYLINOSITOL 4-KINASE BETA	A C CA [auth c] G GA [auth g] A, C, CA [auth c], G, GA [auth g], I, M, O, Q, S, W, Y	566	Homo sapiens	Mutation(s): 1 EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens) Explore Q9UBF8 Go to UniProtKB: Q9UBF8
PHAROS: Q9UBF8 GTEx: ENSG00000143393
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBF8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS-RELATED PROTEIN RAB-11A	B D DA [auth d] H HA [auth h] B, D, DA [auth d], H, HA [auth h], J, N, P, R, T, X, Z	219	Homo sapiens	Mutation(s): 1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491 Go to UniProtKB: P62491
PHAROS: P62491 GTEx: ENSG00000103769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62491
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RAB11 FAMILY-INTERACTING PROTEIN 3	AA [auth a] BA [auth b] E EA [auth e] F AA [auth a], BA [auth b], E, EA [auth e], F, FA [auth f], IA [auth i], JA [auth j], K, L, U, V	48	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75154 (Homo sapiens) Explore O75154 Go to UniProtKB: O75154
PHAROS: O75154 GTEx: ENSG00000090565
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75154
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSP Query on GSP Download Ideal Coordinates CCD File SDF format, chain RA [auth H] SDF format, chain AB [auth P] SDF format, chain DB [auth R] SDF format, chain GB [auth T] SDF format, chain JB [auth X] SDF format, chain LA [auth B] SDF format, chain MB [auth Z] SDF format, chain OA [auth D] SDF format, chain PB [auth d] SDF format, chain SB [auth h] SDF format, chain UA [auth J] SDF format, chain XA [auth N] MOL2 format, chain RA [auth H] MOL2 format, chain AB [auth P] MOL2 format, chain DB [auth R] MOL2 format, chain GB [auth T] MOL2 format, chain JB [auth X] MOL2 format, chain LA [auth B] MOL2 format, chain MB [auth Z] MOL2 format, chain OA [auth D] MOL2 format, chain PB [auth d] MOL2 format, chain SB [auth h] MOL2 format, chain UA [auth J] MOL2 format, chain XA [auth N] mmCIF format, chain RA [auth H] mmCIF format, chain AB [auth P] mmCIF format, chain DB [auth R] mmCIF format, chain GB [auth T] mmCIF format, chain JB [auth X] mmCIF format, chain LA [auth B] mmCIF format, chain MB [auth Z] mmCIF format, chain OA [auth D] mmCIF format, chain PB [auth d] mmCIF format, chain SB [auth h] mmCIF format, chain UA [auth J] mmCIF format, chain XA [auth N]	AB [auth P] DB [auth R] GB [auth T] JB [auth X] LA [auth B] AB [auth P], DB [auth R], GB [auth T], JB [auth X], LA [auth B], MB [auth Z], OA [auth D], PB [auth d], RA [auth H], SB [auth h], UA [auth J], XA [auth N]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ S XOFLBQFBSOEHOG-UUOKFMHZSA-N		Interactions Focus chain AB [auth P] Focus chain DB [auth R] Focus chain GB [auth T] Focus chain JB [auth X] Focus chain LA [auth B] Focus chain MB [auth Z] Focus chain OA [auth D] Focus chain PB [auth d] Focus chain RA [auth H] Focus chain SB [auth h] Focus chain UA [auth J] Focus chain XA [auth N] Interactions & Density Focus chain AB [auth P] Focus chain DB [auth R] Focus chain GB [auth T] Focus chain JB [auth X] Focus chain LA [auth B] Focus chain MB [auth Z] Focus chain OA [auth D] Focus chain PB [auth d] Focus chain RA [auth H] Focus chain SB [auth h] Focus chain UA [auth J] Focus chain XA [auth N]
093 Query on 093 Download Ideal Coordinates CCD File SDF format, chain OB [auth c] SDF format, chain CB [auth Q] SDF format, chain FB [auth S] SDF format, chain IB [auth W] SDF format, chain KA [auth A] SDF format, chain LB [auth Y] SDF format, chain NA [auth C] SDF format, chain QA [auth G] SDF format, chain RB [auth g] SDF format, chain TA [auth I] SDF format, chain WA [auth M] SDF format, chain ZA [auth O] MOL2 format, chain OB [auth c] MOL2 format, chain CB [auth Q] MOL2 format, chain FB [auth S] MOL2 format, chain IB [auth W] MOL2 format, chain KA [auth A] MOL2 format, chain LB [auth Y] MOL2 format, chain NA [auth C] MOL2 format, chain QA [auth G] MOL2 format, chain RB [auth g] MOL2 format, chain TA [auth I] MOL2 format, chain WA [auth M] MOL2 format, chain ZA [auth O] mmCIF format, chain OB [auth c] mmCIF format, chain CB [auth Q] mmCIF format, chain FB [auth S] mmCIF format, chain IB [auth W] mmCIF format, chain KA [auth A] mmCIF format, chain LB [auth Y] mmCIF format, chain NA [auth C] mmCIF format, chain QA [auth G] mmCIF format, chain RB [auth g] mmCIF format, chain TA [auth I] mmCIF format, chain WA [auth M] mmCIF format, chain ZA [auth O]	CB [auth Q] FB [auth S] IB [auth W] KA [auth A] LB [auth Y] CB [auth Q], FB [auth S], IB [auth W], KA [auth A], LB [auth Y], NA [auth C], OB [auth c], QA [auth G], RB [auth g], TA [auth I], WA [auth M], ZA [auth O]	N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE C₁₄ H₁₆ Cl N₃ O₄ S₂ JFVNFXCESCXMBC-UHFFFAOYSA-N		Interactions Focus chain CB [auth Q] Focus chain FB [auth S] Focus chain IB [auth W] Focus chain KA [auth A] Focus chain LB [auth Y] Focus chain NA [auth C] Focus chain OB [auth c] Focus chain QA [auth G] Focus chain RB [auth g] Focus chain TA [auth I] Focus chain WA [auth M] Focus chain ZA [auth O] Interactions & Density Focus chain CB [auth Q] Focus chain FB [auth S] Focus chain IB [auth W] Focus chain KA [auth A] Focus chain LB [auth Y] Focus chain NA [auth C] Focus chain OB [auth c] Focus chain QA [auth G] Focus chain RB [auth g] Focus chain TA [auth I] Focus chain WA [auth M] Focus chain ZA [auth O]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain KB [auth X] SDF format, chain QB [auth d] SDF format, chain BB [auth P] SDF format, chain EB [auth R] SDF format, chain HB [auth T] SDF format, chain MA [auth B] SDF format, chain NB [auth Z] SDF format, chain PA [auth D] SDF format, chain SA [auth H] SDF format, chain TB [auth h] SDF format, chain VA [auth J] SDF format, chain YA [auth N] MOL2 format, chain KB [auth X] MOL2 format, chain QB [auth d] MOL2 format, chain BB [auth P] MOL2 format, chain EB [auth R] MOL2 format, chain HB [auth T] MOL2 format, chain MA [auth B] MOL2 format, chain NB [auth Z] MOL2 format, chain PA [auth D] MOL2 format, chain SA [auth H] MOL2 format, chain TB [auth h] MOL2 format, chain VA [auth J] MOL2 format, chain YA [auth N] mmCIF format, chain KB [auth X] mmCIF format, chain QB [auth d] mmCIF format, chain BB [auth P] mmCIF format, chain EB [auth R] mmCIF format, chain HB [auth T] mmCIF format, chain MA [auth B] mmCIF format, chain NB [auth Z] mmCIF format, chain PA [auth D] mmCIF format, chain SA [auth H] mmCIF format, chain TB [auth h] mmCIF format, chain VA [auth J] mmCIF format, chain YA [auth N]	BB [auth P] EB [auth R] HB [auth T] KB [auth X] MA [auth B] BB [auth P], EB [auth R], HB [auth T], KB [auth X], MA [auth B], NB [auth Z], PA [auth D], QB [auth d], SA [auth H], TB [auth h], VA [auth J], YA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth P] Focus chain EB [auth R] Focus chain HB [auth T] Focus chain KB [auth X] Focus chain MA [auth B] Focus chain NB [auth Z] Focus chain PA [auth D] Focus chain QB [auth d] Focus chain SA [auth H] Focus chain TB [auth h] Focus chain VA [auth J] Focus chain YA [auth N] Interactions & Density Focus chain BB [auth P] Focus chain EB [auth R] Focus chain HB [auth T] Focus chain KB [auth X] Focus chain MA [auth B] Focus chain NB [auth Z] Focus chain PA [auth D] Focus chain QB [auth d] Focus chain SA [auth H] Focus chain TB [auth h] Focus chain VA [auth J] Focus chain YA [auth N]

Binding Affinity Annotations
ID	Source	Binding Affinity
093	BindingDB: 4D0M	IC50: min: 19, max: 28 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 6.00 Å
R-Value Free: 0.359
R-Value Work: 0.253
R-Value Observed: 0.259
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.504	α = 90
b = 134.465	β = 90.33
c = 294.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2014-06-11
Changes: Database references
Version 1.2: 2014-06-18
Changes: Derived calculations
Version 1.3: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2018-11-21
Changes: Advisory, Data collection, Derived calculations
Version 1.5: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description