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- PDB-5kyu: crystal structure of Sec23 and TANGO1 peptide2 complex -

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Basic information

Entry
Database: PDB / ID: 5kyu
Titlecrystal structure of Sec23 and TANGO1 peptide2 complex
Components
  • Protein transport protein Sec23A
  • Protein transport protein Sec24D
  • TANGO1 peptide2
KeywordsPROTEIN TRANSPORT / COPII coat / collagen secretion / cargo adapter / vesicle
Function / homology
Function and homology information


vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / COPII-coated vesicle cargo loading / cellular response to oxidised low-density lipoprotein particle stimulus / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion ...vesicle cargo loading / negative regulation of lymphocyte migration / protein localization to endoplasmic reticulum exit site / COPII-coated vesicle cargo loading / cellular response to oxidised low-density lipoprotein particle stimulus / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / negative regulation of leukocyte cell-cell adhesion / negative regulation of cell adhesion / endoplasmic reticulum organization / cell migration involved in sprouting angiogenesis / positive regulation of leukocyte migration / COPII-mediated vesicle transport / cargo receptor activity / lipoprotein transport / endoplasmic reticulum exit site / exocytosis / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class II antigen presentation / GTPase activator activity / negative regulation of cell migration / SNARE binding / protein localization to plasma membrane / Post-translational protein phosphorylation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / wound healing / ER to Golgi transport vesicle membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / protein transport / in utero embryonic development / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / zinc ion binding / membrane / 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 / 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 / Variant SH3 domain / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Transport and Golgi organization protein 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.512 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 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein transport protein Sec23A
B: Protein transport protein Sec24D
C: TANGO1 peptide2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6005
Polymers173,4693
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-14 kcal/mol
Surface area62220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.428, 140.926, 150.603
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 / Fragment: unp residues 1-765
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: 86388.531 Da / Num. of mol.: 1 / Fragment: unp residues 266-1032
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: Protein/peptide TANGO1 peptide2


Mass: 830.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JRA6*PLUS
#4: 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: 3.5→50 Å / Num. obs: 27343 / % possible obs: 97.8 % / Redundancy: 4.1 % / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EFO

3efo


Resolution: 3.512→48.548 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 1998 7.31 %
Rwork0.217 --
obs0.2206 27343 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.512→48.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11603 0 2 0 11605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211940
X-RAY DIFFRACTIONf_angle_d0.5416180
X-RAY DIFFRACTIONf_dihedral_angle_d10.9147252
X-RAY DIFFRACTIONf_chiral_restr0.0421805
X-RAY DIFFRACTIONf_plane_restr0.0042103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5118-3.59960.35171210.34341581X-RAY DIFFRACTION86
3.5996-3.69690.38381370.31291778X-RAY DIFFRACTION97
3.6969-3.80560.35161350.29481739X-RAY DIFFRACTION95
3.8056-3.92840.32071470.25981793X-RAY DIFFRACTION99
3.9284-4.06880.30251410.24791841X-RAY DIFFRACTION99
4.0688-4.23160.25421400.23481802X-RAY DIFFRACTION98
4.2316-4.4240.29161550.21291841X-RAY DIFFRACTION99
4.424-4.65710.25921410.20561819X-RAY DIFFRACTION99
4.6571-4.94860.26661400.19871820X-RAY DIFFRACTION98
4.9486-5.33030.24761390.19661803X-RAY DIFFRACTION97
5.3303-5.86590.29081520.21951863X-RAY DIFFRACTION99
5.8659-6.71280.28951490.24091865X-RAY DIFFRACTION99
6.7128-8.45010.24741430.2131841X-RAY DIFFRACTION97
8.4501-48.55310.21361580.17131959X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.408-0.4381-1.18755.4827-1.71114.92480.377-0.26640.96090.1761-0.05640.8351-0.6364-0.2559-0.3740.9563-0.04120.19520.7808-0.05011.2861-75.620496.7981-7.5817
24.7816-3.64030.19929.2969-0.17111.57790.2598-0.6592-0.19780.9119-0.2016-0.37340.37110.0936-0.00641.1604-0.2228-0.06771.15910.12470.8746-54.025469.0564-1.2557
36.14150.1671-0.11332.9591-0.03724.61720.3977-0.4759-0.73190.4658-0.24240.33380.2986-0.09110.14921.34-0.0843-0.10580.95980.00121.3299-59.363152.8444-2.252
42.6147-3.4698-4.36245.3345.42857.53790.7735-2.43610.69890.20450.3601-0.35010.9790.6606-1.12931.5751-0.236-0.33691.62470.01380.8499-53.965459.10427.6024
55.96050.03770.17542.5045-2.43422.3956-0.13140.2951-0.88110.5133-0.6001-1.27211.21290.80090.90911.50170.13570.17241.39430.36021.7596-43.077250.1959-14.3161
61.6411-0.2465-0.88323.25910.78423.45650.1850.60990.5154-0.402-0.2653-0.08160.0867-0.04410.11410.9929-0.003-0.05781.02660.17720.9433-55.63763.1012-18.2869
79.1475-2.2778-2.89194.451-0.28473.4046-0.0045-1.43310.7013-0.0681-0.05340.4755-0.1510.42440.13561.1901-0.0565-0.23321.1404-0.0431.3497-53.616478.1234-2.5995
82.51440.33190.82093.1051-4.48186.71120.243-0.04520.18730.29340.08080.2359-0.22310.2379-0.35080.9112-0.13730.03570.8618-0.01031.2264-74.162583.5545-18.3045
94.5755-2.8482-0.9577.7581-2.62673.64530.20110.27670.8230.61430.28870.8591-0.9255-0.5515-0.24840.9316-0.0564-0.08511.0018-0.10031.6059-68.792492.3988-17.047
105.8774-1.28290.08112.0715-2.53049.53511.08352.55540.1116-1.4564-0.74440.20910.33120.6198-0.34261.13620.307-0.24271.95810.39621.3104-61.346495.9506-39.6376
114.9676-0.92811.96971.11870.09331.86620.12220.32081.1825-0.4929-0.1889-0.59870.08130.22010.15721.05490.10760.21281.22820.37141.3509-45.344289.0239-25.0802
129.87831.5372-0.17488.44312.69756.06780.48670.43630.52310.48790.5851-1.88940.06850.5106-1.11140.98620.0486-0.08581.23180.31981.7607-28.916588.6966-18.0588
131.75441.6378-0.15441.5258-0.14760.00590.2009-0.051-0.1582-1.7011.12910.50251.761-1.1621-0.83932.0082-0.16990.03222.25370.3671.4112-51.249787.6952-43.6921
141.15770.13280.39186.4132-1.16526.60170.5721.44810.4125-0.53370.43550.2233-2.77060.2064-0.47662.06050.43520.4071.86190.44450.9456-53.816397.7411-43.687
155.5697-0.9839-1.38893.7521-0.48882.65440.19270.3913-0.6815-0.6122-0.4709-0.68180.02520.51560.31041.11890.19560.05981.1010.00280.9692-41.2984-4.6701-14.1294
161.7451-0.23-0.19715.60260.32051.09750.03480.2939-0.13650.0388-0.29090.4376-0.2358-0.02260.26250.86670.0303-0.09720.90920.06990.8637-56.794717.584-4.4513
172.3983-0.55130.53263.21580.57096.57530.1998-0.3491-0.3170.8899-0.10520.61170.4416-0.4824-0.04351.1639-0.08160.14441.06860.10091.3727-65.571-2.232612.9003
186.24661.7029-4.83738.3043-9.08681.9934-0.9872-0.6048-2.9508-3.5115-3.29151.30633.3515-1.54583.09993.307-1.4022-0.28072.549-0.80913.0736-77.4619-16.1523-3.7673
192.31963.2650.83174.61290.99351.7595-0.1097-0.2845-0.14611.4355-1.23222.58250.1462-0.46051.47856.5004-0.7563-1.06811.8861-0.57344.0132-77.2297-22.8372-16.6709
200.7157-0.7652-1.29030.97541.41872.3297-0.14740.2154-0.404-0.38030.4552-0.30660.1396-0.1857-0.18343.0534-1.4188-1.39282.5070.88314.9062-16.0959100.5686-22.1033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:114 )A3 - 114
2X-RAY DIFFRACTION2( CHAIN A AND RESID 115:157 )A115 - 157
3X-RAY DIFFRACTION3( CHAIN A AND RESID 158:209 )A158 - 209
4X-RAY DIFFRACTION4( CHAIN A AND RESID 226:245 )A226 - 245
5X-RAY DIFFRACTION5( CHAIN A AND RESID 246:263 )A246 - 263
6X-RAY DIFFRACTION6( CHAIN A AND RESID 264:379 )A264 - 379
7X-RAY DIFFRACTION7( CHAIN A AND RESID 380:407 )A380 - 407
8X-RAY DIFFRACTION8( CHAIN A AND RESID 408:464 )A408 - 464
9X-RAY DIFFRACTION9( CHAIN A AND RESID 475:535 )A475 - 535
10X-RAY DIFFRACTION10( CHAIN A AND RESID 536:571 )A536 - 571
11X-RAY DIFFRACTION11( CHAIN A AND RESID 572:661 )A572 - 661
12X-RAY DIFFRACTION12( CHAIN A AND RESID 662:722 )A662 - 722
13X-RAY DIFFRACTION13( CHAIN A AND RESID 741:748 )A741 - 748
14X-RAY DIFFRACTION14( CHAIN A AND RESID 749:762 )A749 - 762
15X-RAY DIFFRACTION15( CHAIN B AND RESID 267:435 )B267 - 435
16X-RAY DIFFRACTION16( CHAIN B AND RESID 436:820 )B436 - 820
17X-RAY DIFFRACTION17( CHAIN B AND RESID 821:1010 )B821 - 1010
18X-RAY DIFFRACTION18( CHAIN B AND RESID 1014:1028 )B1014 - 1028
19X-RAY DIFFRACTION19( CHAIN B AND RESID 1029:1033 )B1029 - 1033
20X-RAY DIFFRACTION20( CHAIN C AND RESID 1801:1803 )C1801 - 1803

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