4V0N | pdb_00004v0n

Crystal structure of BBS1N in complex with ARL6DN, soaked with mercury

PDB DOI: https://doi.org/10.2210/pdb4V0N/pdb

Classification: HYDROLASE/STRUCTURAL PROTEIN
Organism(s): Chlamydomonas reinhardtii
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2014-09-17 Released: 2014-11-19
Deposition Author(s): Mourao, A., Lorentzen, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free:
0.249 (Depositor), 0.259 (DCC)
R-Value Work:
0.213 (Depositor), 0.229 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis for Membrane Targeting of the Bbsome by Arl6

Mourao, A., Nager, A.R., Nachury, M.V., Lorentzen, E.

(2014) Nat Struct Mol Biol 21: 1035

PubMed: 25402481 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2920
Primary Citation Related Structures:
4V0K, 4V0L, 4V0M, 4V0N, 4V0O

PubMed Abstract:
The BBSome is a coat-like ciliary trafficking complex composed of proteins mutated in Bardet-Biedl syndrome (BBS). A critical step in BBSome-mediated sorting is recruitment of the BBSome to membranes by the GTP-bound Arf-like GTPase ARL6. We have determined crystal structures of Chlamydomonas reinhardtii ARL6-GDP, ARL6-GTP and the ARL6-GTP-BBS1 complex. The structures demonstrate how ARL6-GTP binds the BBS1 β-propeller at blades 1 and 7 and explain why GTP- but not GDP-bound ARL6 can recruit the BBSome to membranes. Single point mutations in the ARL6-GTP-BBS1 interface abolish the interaction of ARL6 with the BBSome and prevent the import of BBSomes into cilia. Furthermore, we show that BBS1 with the M390R mutation, responsible for 30% of all reported BBS disease cases, fails to interact with ARL6-GTP, thus providing a molecular rationale for patient pathologies.

Organizational Affiliation

Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 274.32 kDa
Atom Count: 14,532
Modeled Residue Count: 1,927
Deposited Residue Count: 2,376
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARF-LIKE SMALL GTPASE	A, C, E, G	169	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8JF99 (Chlamydomonas reinhardtii) Explore A8JF99 Go to UniProtKB: A8JF99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8JF99
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BARDET-BIEDL SYNDROME 1 PROTEIN	B, D, F, H	425	Chlamydomonas reinhardtii	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain EB [auth G] SDF format, chain I [auth A] SDF format, chain NA [auth E] SDF format, chain Y [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain Y [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain I [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain Y [auth C]	EB [auth G], I [auth A], NA [auth E], Y [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain EB [auth G] Focus chain I [auth A] Focus chain NA [auth E] Focus chain Y [auth C] Interactions & Density Focus chain EB [auth G] Focus chain I [auth A] Focus chain NA [auth E] Focus chain Y [auth C]
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain YA [auth F] SDF format, chain XA [auth F] SDF format, chain X [auth B] SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain UB [auth H] SDF format, chain UA [auth F] SDF format, chain U [auth B] SDF format, chain TB [auth H] SDF format, chain TA [auth F] SDF format, chain T [auth B] SDF format, chain SB [auth H] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain RB [auth H] SDF format, chain RA [auth F] SDF format, chain R [auth B] SDF format, chain QB [auth H] SDF format, chain QA [auth F] SDF format, chain Q [auth B] SDF format, chain PB [auth H] SDF format, chain PA [auth E] SDF format, chain P [auth B] SDF format, chain OB [auth H] SDF format, chain O [auth B] SDF format, chain NB [auth H] SDF format, chain N [auth B] SDF format, chain MB [auth H] SDF format, chain MA [auth D] SDF format, chain M [auth B] SDF format, chain LB [auth H] SDF format, chain LA [auth D] SDF format, chain L [auth B] SDF format, chain KB [auth H] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JB [auth H] SDF format, chain JA [auth D] SDF format, chain IB [auth H] SDF format, chain IA [auth D] SDF format, chain HB [auth H] SDF format, chain HA [auth D] SDF format, chain GB [auth G] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DB [auth F] SDF format, chain DA [auth D] SDF format, chain CB [auth F] SDF format, chain CA [auth D] SDF format, chain BB [auth F] SDF format, chain BA [auth D] SDF format, chain AB [auth F] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain UB [auth H] MOL2 format, chain UA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TB [auth H] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth H] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain RB [auth H] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain QB [auth H] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain PB [auth H] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain OB [auth H] MOL2 format, chain O [auth B] MOL2 format, chain NB [auth H] MOL2 format, chain N [auth B] MOL2 format, chain MB [auth H] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain LB [auth H] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain KB [auth H] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth F] MOL2 format, chain DA [auth D] MOL2 format, chain CB [auth F] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth F] MOL2 format, chain BA [auth D] MOL2 format, chain AB [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain UB [auth H] mmCIF format, chain UA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TB [auth H] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth H] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain RB [auth H] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain QB [auth H] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain PB [auth H] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain OB [auth H] mmCIF format, chain O [auth B] mmCIF format, chain NB [auth H] mmCIF format, chain N [auth B] mmCIF format, chain MB [auth H] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain LB [auth H] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain KB [auth H] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth F] mmCIF format, chain DA [auth D] mmCIF format, chain CB [auth F] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth F] mmCIF format, chain BA [auth D] mmCIF format, chain AB [auth F] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth F] BA [auth D] BB [auth F] CA [auth D] AA [auth C], AB [auth F], BA [auth D], BB [auth F], CA [auth D], CB [auth F], DA [auth D], DB [auth F], EA [auth D], FA [auth D], GA [auth D], GB [auth G], HA [auth D], HB [auth H], IA [auth D], IB [auth H], JA [auth D], JB [auth H], K [auth A], KA [auth D], KB [auth H], L [auth B], LA [auth D], LB [auth H], M [auth B], MA [auth D], MB [auth H], N [auth B], NB [auth H], O [auth B], OB [auth H], P [auth B], PA [auth E], PB [auth H], Q [auth B], QA [auth F], QB [auth H], R [auth B], RA [auth F], RB [auth H], S [auth B], SA [auth F], SB [auth H], T [auth B], TA [auth F], TB [auth H], U [auth B], UA [auth F], UB [auth H], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], YA [auth F], ZA [auth F]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth D] Focus chain BB [auth F] Focus chain CA [auth D] Focus chain CB [auth F] Focus chain DA [auth D] Focus chain DB [auth F] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain L [auth B] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain M [auth B] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain N [auth B] Focus chain NB [auth H] Focus chain O [auth B] Focus chain OB [auth H] Focus chain P [auth B] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth F] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth D] Focus chain BB [auth F] Focus chain CA [auth D] Focus chain CB [auth F] Focus chain DA [auth D] Focus chain DB [auth F] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth H] Focus chain L [auth B] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain M [auth B] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain N [auth B] Focus chain NB [auth H] Focus chain O [auth B] Focus chain OB [auth H] Focus chain P [auth B] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth F] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain OA [auth E] SDF format, chain J [auth A] SDF format, chain FB [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain OA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain FB [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain OA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain FB [auth G]	FB [auth G], J [auth A], OA [auth E], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain J [auth A] Focus chain OA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain FB [auth G] Focus chain J [auth A] Focus chain OA [auth E] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free: 0.249 (Depositor), 0.259 (DCC)
R-Value Work: 0.213 (Depositor), 0.229 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.745	α = 90
b = 123.745	β = 90
c = 443.709	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Mourao, A.

Lorentzen, E.

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2014-11-26
Changes: Database references
Version 1.2: 2014-12-17
Changes: Database references
Version 1.3: 2019-04-03
Changes: Data collection, Other, Source and taxonomy
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Other, Structure summary