2IFU

Crystal Structure of a Gamma-SNAP from Danio rerio

PDB DOI: https://doi.org/10.2210/pdb2IFU/pdb

Classification: ENDOCYTOSIS/EXOCYTOSIS
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-09-21 Released: 2006-10-10
Deposition Author(s): Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., Mccoy, J.G., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.261
R-Value Work: 0.239
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

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

Literature

Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family.

Bitto, E., Bingman, C.A., Kondrashov, D.A., McCoy, J.G., Bannen, R.M., Wesenberg, G.E., Phillips, G.N.

(2008) Proteins 70: 93-104

PubMed: 17634982 Search on PubMed
DOI: https://doi.org/10.1002/prot.21468
Primary Citation of Related Structures:
2IFU

PubMed Abstract:
Soluble N-ethylmaleimide-sensitive factor attachment protein gamma (gamma-SNAP) is a member of an eukaryotic protein family involved in intracellular membrane trafficking. The X-ray structure of Brachydanio rerio gamma-SNAP was determined to 2.6 A and revealed an all-helical protein comprised of an extended twisted-sheet of helical hairpins with a helical-bundle domain on its carboxy-terminal end. Structural and conformational differences between multiple observed gamma-SNAP molecules and Sec17, a SNAP family protein from yeast, are analyzed. Conformational variation in gamma-SNAP molecules is matched with great precision by the two lowest frequency normal modes of the structure. Comparison of the lowest-frequency modes from gamma-SNAP and Sec17 indicated that the structures share preferred directions of flexibility, corresponding to bending and twisting of the twisted sheet motif. We discuss possible consequences related to the flexibility of the SNAP proteins for the mechanism of the 20S complex disassembly during the SNAP receptors recycling.

Organizational Affiliation

Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.

Macromolecule Content

Total Structure Weight: 139.3 kDa
Atom Count: 8,758
Modelled Residue Count: 1,092
Deposited Residue Count: 1,228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-snap	A, B, C, D	307	Danio rerio	Mutation(s): 10 Gene Names: zgc:110177
UniProt
Find proteins for Q5BJK3 (Danio rerio) Explore Q5BJK3 Go to UniProtKB: Q5BJK3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5BJK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.261
R-Value Work: 0.239
R-Value Observed: 0.240
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.378	α = 90
b = 90.813	β = 90
c = 264.173	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
Type: Initial release
Version 1.1: 2008-01-15
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary