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- PDB-5kyy: Crystal structure of Sec23 and TANGO1 peptide4 complex -

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Basic information

Entry
Database: PDB / ID: 5kyy
TitleCrystal structure of Sec23 and TANGO1 peptide4 complex
Components
  • Protein transport protein Sec23A
  • Protein transport protein Sec24D
KeywordsPROTEIN TRANSPORT / COPII coat / collagen secretion / cargo adapter / vesicle
Function / homology
Function and homology information


COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / GTPase activator activity / SNARE binding ...COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / in utero embryonic development / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / cytosol
Similarity search - Function
Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / : / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain ...Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Protein transport protein Sec23 / Sec23, C-terminal / : / Zn-finger domain of Sec23/24 / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein transport protein Sec24D / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.403 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: TANGO1/cTAGE5 receptor as a polyvalent template for assembly of large COPII coats.
Authors: Ma, W. / Goldberg, J.
History
DepositionJul 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,0284
Polymers172,8972
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area61820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.386, 139.056, 149.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein transport protein Sec23A / SEC23-related protein A


Mass: 86249.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15436
#2: Protein Protein transport protein Sec24D / SEC24-related protein D


Mass: 86647.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D, KIAA0755
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O94855
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.5, 5.5 %(w/v) PEG 4000, 100 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24866 / % possible obs: 99.8 % / Redundancy: 3.5 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.403→48.006 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1985 7.98 %
Rwork0.1769 --
obs0.1829 24866 83.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.403→48.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11680 0 2 0 11682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111984
X-RAY DIFFRACTIONf_angle_d1.36716229
X-RAY DIFFRACTIONf_dihedral_angle_d17.9044489
X-RAY DIFFRACTIONf_chiral_restr0.0521806
X-RAY DIFFRACTIONf_plane_restr0.0072109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4032-3.48820.32621380.25751564X-RAY DIFFRACTION82
3.4882-3.58250.34231330.24091579X-RAY DIFFRACTION83
3.5825-3.68790.3121500.22351542X-RAY DIFFRACTION81
3.6879-3.80690.27841180.20961507X-RAY DIFFRACTION78
3.8069-3.94290.24261360.1931675X-RAY DIFFRACTION86
3.9429-4.10070.26681490.17921683X-RAY DIFFRACTION87
4.1007-4.28720.27381460.17491651X-RAY DIFFRACTION86
4.2872-4.51310.20561370.16031650X-RAY DIFFRACTION85
4.5131-4.79560.22581440.15191632X-RAY DIFFRACTION84
4.7956-5.16550.2581420.1531578X-RAY DIFFRACTION81
5.1655-5.68460.27291560.17041733X-RAY DIFFRACTION89
5.6846-6.50540.26691480.18431718X-RAY DIFFRACTION87
6.5054-8.18950.25281380.17571639X-RAY DIFFRACTION82
8.1895-48.0110.2011500.15391730X-RAY DIFFRACTION83

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