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- PDB-4l9o: Crystal Structure of the Sec13-Sec16 blade-inserted complex from ... -

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Basic information

Entry
Database: PDB / ID: 4l9o
TitleCrystal Structure of the Sec13-Sec16 blade-inserted complex from Pichia pastoris
ComponentsSec16,Protein transport protein SEC13
KeywordsPROTEIN TRANSPORT / Beta propeller / COPII / Vesicle coat budding / Nuclear Pore Complex Proteins / COP-coated Vesicles / Endoplasmic Reticulum / ACE1
Function / homology
Function and homology information


GATOR2 complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to endoplasmic reticulum exit site / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / Golgi organization ...GATOR2 complex / positive regulation of ER to Golgi vesicle-mediated transport / protein localization to endoplasmic reticulum exit site / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / COPII vesicle coat / Golgi organization / endoplasmic reticulum exit site / mRNA transport / intracellular transport / vesicle-mediated transport / ERAD pathway / positive regulation of TORC1 signaling / ER to Golgi transport vesicle membrane / autophagy / protein import into nucleus / protein transport / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity
Similarity search - Function
Sec16, central conserved domain / Vesicle coat trafficking protein Sec16 mid-region / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. ...Sec16, central conserved domain / Vesicle coat trafficking protein Sec16 mid-region / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Protein transport protein SEC13 / Protein transport protein sec16
Similarity search - Component
Biological speciesKomagataella pastoris (fungus)
Komagataella phaffii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMcMahon, C. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: Mol Biol Cell / Year: 2013
Title: Sec16 influences transitional ER sites by regulating rather than organizing COPII.
Authors: Bharucha, N. / Liu, Y. / Papanikou, E. / McMahon, C. / Esaki, M. / Jeffrey, P.D. / Hughson, F.M. / Glick, B.S.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sec16,Protein transport protein SEC13
B: Sec16,Protein transport protein SEC13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47212
Polymers76,9702
Non-polymers50110
Water5,386299
1
A: Sec16,Protein transport protein SEC13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94710
Polymers38,4851
Non-polymers4619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sec16,Protein transport protein SEC13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5252
Polymers38,4851
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.509, 49.320, 90.904
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sec16,Protein transport protein SEC13


Mass: 38485.137 Da / Num. of mol.: 2
Fragment: unp residues 2-289, unp residues 1030-1076,unp residues 2-289, unp residues 1030-1076,unp residues 2-289, unp residues 1030-1076,unp residues 2-289, unp residues 1030-1076
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella pastoris (fungus), (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Gene: SEC16, SEC13, PAS_chr1-3_0057 / Plasmid: pET28a / Strain: GS115 / ATCC 20864 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q45TY0, UniProt: P53024
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% (w/v) PEG 3350, 200 mM calcium chloride, 200 mM sodium thiocyanate, 100 mM Tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. all: 82989 / Num. obs: 82989 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Χ2: 1.24 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.615.60.6877581.042193.2
1.61-1.676.50.54782821.048199.8
1.67-1.756.90.40783141.0521100
1.75-1.8470.28583021.0671100
1.84-1.957.10.17783281.1691100
1.95-2.17.20.12482861.3061100
2.1-2.327.20.10683721.3161100
2.32-2.657.20.09483311.371100
2.65-3.347.10.06984411.4891100
3.34-1007.30.05185751.433199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3JRP

3jrp


Resolution: 1.6→44.419 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8683 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 3872 5.04 %RANDOM THROUGHOUT
Rwork0.1728 ---
obs0.1744 76779 99.82 %-
all-76779 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 26.809 Å2 / Biso min: 7.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 25 299 5356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115193
X-RAY DIFFRACTIONf_angle_d1.3187055
X-RAY DIFFRACTIONf_chiral_restr0.086754
X-RAY DIFFRACTIONf_plane_restr0.007883
X-RAY DIFFRACTIONf_dihedral_angle_d13.5711813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61950.30331470.25342506265398
1.6195-1.640.25461420.23262599274199
1.64-1.66160.24631400.219725582698100
1.6616-1.68440.26211390.210226052744100
1.6844-1.70840.2381250.207325972722100
1.7084-1.73390.25031360.197125482684100
1.7339-1.7610.22041420.188526212763100
1.761-1.78990.2591270.18425772704100
1.7899-1.82080.23611210.176626302751100
1.8208-1.85390.17231230.165225922715100
1.8539-1.88950.20881370.16226032740100
1.8895-1.92810.19021370.156725822719100
1.9281-1.970.19511460.154625932739100
1.97-2.01590.17851450.151125952740100
2.0159-2.06630.20791380.147326042742100
2.0663-2.12210.18281250.151225902715100
2.1221-2.18460.20571410.157225912732100
2.1846-2.25510.20541600.163126052765100
2.2551-2.33570.19511440.172326012745100
2.3357-2.42920.23521640.179625782742100
2.4292-2.53970.20781380.166926052743100
2.5397-2.67360.20451450.170426062751100
2.6736-2.84110.18161230.166126372760100
2.8411-3.06040.19971440.175726312775100
3.0604-3.36830.19671380.167126242762100
3.3683-3.85550.20481410.17326342775100
3.8555-4.85650.1891250.157826682793100
4.8565-44.43590.19251390.200927272866100

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