PROTEIN TRANSPORT / alpha-helical-stack / beta-propeller
Function / homology
Function and homology information
Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / SUMOylation of RNA binding proteins / endoplasmic reticulum organization / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / endoplasmic reticulum exit site / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / intracellular protein transport / protein import into nucleus / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #980 / Helix Hairpins - #1600 / N-terminal domain of TfIIb - #400 / Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #980 / Helix Hairpins - #1600 / N-terminal domain of TfIIb - #400 / Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / N-terminal domain of TfIIb / Helix Hairpins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Single Sheet / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
A: Protein transport protein SEC13 B: Protein transport protein SEC31 C: Protein transport protein SEC13 D: Protein transport protein SEC31 E: Protein transport protein SEC13 F: Protein transport protein SEC31 G: Protein transport protein SEC13 H: Protein transport protein SEC31
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-ID
ID
Operator
Domain-ID
Fraction
1
1
H, K, L
1
0.772
1
1
-h,-k,l
2
0.228
Reflection
Resolution: 2.8→30 Å / Num. obs: 69366 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.6
Reflection shell
Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.477 / % possible all: 99.4
-
Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
PHASER
phasing
REFMAC
5.5.0109
refinement
XDS
datareduction
XSCALE
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.38 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.842 / SU B: 19.803 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29962
1792
2.6 %
RANDOM
Rwork
0.26715
-
-
-
obs
0.26801
67561
99.6 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 51.777 Å2
Baniso -1
Baniso -2
Baniso -3
1-
43.29 Å2
0 Å2
3.26 Å2
2-
-
-19.49 Å2
0 Å2
3-
-
-
-23.81 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→29.38 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
19212
0
0
0
19212
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.022
19597
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.936
1.945
26580
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.904
5
2412
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.106
25.43
884
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.344
15
3442
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.45
15
68
X-RAY DIFFRACTION
r_chiral_restr
0.059
0.2
2999
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
14588
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.512
1.5
12072
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.938
2
19463
X-RAY DIFFRACTION
r_scbond_it
0.602
3
7525
X-RAY DIFFRACTION
r_scangle_it
1.139
4.5
7117
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
2196
MEDIUMPOSITIONAL
0.21
0.5
1
2
C
2196
MEDIUMPOSITIONAL
0.22
0.5
1
3
E
2196
MEDIUMPOSITIONAL
0.23
0.5
1
4
G
2196
MEDIUMPOSITIONAL
0.23
0.5
1
1
A
2196
MEDIUMTHERMAL
0.16
2
1
2
C
2196
MEDIUMTHERMAL
0.19
2
1
3
E
2196
MEDIUMTHERMAL
0.18
2
1
4
G
2196
MEDIUMTHERMAL
0.18
2
2
1
B
2596
MEDIUMPOSITIONAL
0.36
0.5
2
2
D
2596
MEDIUMPOSITIONAL
0.37
0.5
2
3
F
2596
MEDIUMPOSITIONAL
0.38
0.5
2
4
H
2596
MEDIUMPOSITIONAL
0.37
0.5
2
1
B
2596
MEDIUMTHERMAL
0.12
2
2
2
D
2596
MEDIUMTHERMAL
0.12
2
2
3
F
2596
MEDIUMTHERMAL
0.12
2
2
4
H
2596
MEDIUMTHERMAL
0.12
2
+
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