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- PDB-5vnm: Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylb... -

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Basic information

Entry
Database: PDB / ID: 5vnm
TitleCrystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (15mM soaking)
Components
  • (Protein transport protein ...) x 2
  • Vesicle-trafficking protein SEC22b
KeywordsPROTEIN TRANSPORT / COPII / Trafficking / p24 / ER retention
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / regulation of cholesterol transport / COPI-dependent Golgi-to-ER retrograde traffic / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity ...Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle fusion with Golgi apparatus / COPI-coated vesicle / regulation of cholesterol transport / COPI-dependent Golgi-to-ER retrograde traffic / COPII-coated vesicle cargo loading / negative regulation of autophagosome assembly / SNARE complex / SNAP receptor activity / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / COPII-mediated vesicle transport / ER-Phagosome pathway / endoplasmic reticulum exit site / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / cholesterol homeostasis / protein localization to plasma membrane / positive regulation of protein secretion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of protein catabolic process / melanosome / protein transport / synaptic vesicle / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / zinc ion binding / cytosol
Similarity search - Function
Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Protein transport protein Sec23 / Sec23, C-terminal ...Vesicle-trafficking protein Sec22 / Longin domain / Longin domain profile. / Sec23/Sec24 helical domain / beta-sandwich domain of Sec23/24 / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / 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 / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Gelsolin-like domain superfamily / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / Longin-like domain superfamily / von Willebrand factor, type A domain / ADF-H/Gelsolin-like domain superfamily / Beta-Lactamase / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-PHENYL-BUTANOIC ACID / Vesicle-trafficking protein SEC22b / Protein transport protein Sec24A / Protein transport protein Sec23A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.765 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Elife / Year: 2017
Title: ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.
Authors: Ma, W. / Goldberg, E. / Goldberg, J.
History
DepositionApr 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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

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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 Sec24A
C: Vesicle-trafficking protein SEC22b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,8426
Polymers188,5473
Non-polymers2953
Water72140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.183, 96.800, 130.609
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein transport protein ... , 2 types, 2 molecules AB

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


Mass: 86178.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15436
#2: Protein Protein transport protein Sec24A / SEC24-related protein A


Mass: 84336.820 Da / Num. of mol.: 1 / Fragment: UNP residues 346-1093
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24A / Cell line (production host): Hi-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95486

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Protein , 1 types, 1 molecules C

#3: Protein Vesicle-trafficking protein SEC22b / ER-Golgi SNARE of 24 kDa / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle- ...ER-Golgi SNARE of 24 kDa / ERS24 / SEC22 vesicle-trafficking protein homolog B / SEC22 vesicle-trafficking protein-like 1 / mSec22b


Mass: 18031.645 Da / Num. of mol.: 1 / Fragment: UNP residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sec22b, Sec22l1 / Production host: Escherichia coli (E. coli) / References: UniProt: O08547

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Non-polymers , 3 types, 43 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CLT / 4-PHENYL-BUTANOIC ACID / GAMMA-PHENYL-BUTYRIC ACID


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 50mM HEPES PH 7.8, 0.5M NaAc and 12% PEG4K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.765→130.608 Å / Num. obs: 43047 / % possible obs: 99.3 % / Redundancy: 3.7 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NUT

2nut


Resolution: 2.765→130.608 Å / SU ML: 0.61 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 35.47
RfactorNum. reflection% reflection
Rfree0.2968 1966 4.57 %
Rwork0.2678 --
obs0.2691 43047 90.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.765→130.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12392 0 14 40 12446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212709
X-RAY DIFFRACTIONf_angle_d0.55317215
X-RAY DIFFRACTIONf_dihedral_angle_d12.2137740
X-RAY DIFFRACTIONf_chiral_restr0.0411946
X-RAY DIFFRACTIONf_plane_restr0.0042225
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)
13.0359-0.0862-1.47854.4134-0.98642.023-0.15170.8206-0.1679-0.35160.0068-0.05760.985-0.82510.16271.31880.03580.14210.9945-0.2410.600729.6444-115.3005-4.9739
23.7941.7908-1.71072.7223-2.18351.7608-0.49970.38320.4972-0.97230.2091-0.50960.35350.05830.2991.49270.14740.26110.8529-0.02520.964840.4578-94.3156-9.2044
33.0674-0.6249-0.65933.26141.06072.49970.20140.25350.4379-0.468-0.24230.0314-0.3537-0.18490.06030.49810.1831-0.01260.5295-0.02290.586318.4684-82.812620.7433
41.6590.0168-0.94923.79750.51633.392-0.20170.284-0.1379-0.3994-0.02670.26340.4227-0.35240.14870.45530.2283-0.06370.5958-0.07590.549311.7515-94.111619.6412
53.42650.7992-1.96453.8247-0.56743.8365-0.26740.74490.5302-1.0965-0.54690.67070.0525-1.35120.22481.31230.3241-0.0151.0603-0.02260.873918.4817-98.4266-1.6732
61.73030.22680.49631.1712-1.42112.2219-0.05810.6911-0.3152-1.5569-0.042-0.07410.25930.10780.02091.20350.19060.15081.0582-0.08290.569330.133-106.0659-4.875
72.30180.6147-1.20732.59160.85573.62610.00750.3366-0.4407-0.4347-0.21070.34990.5758-0.2060.20481.01950.01610.0330.5835-0.15810.701918.6545-121.767810.2181
83.0922-1.31010.03074.4287-0.06634.65780.1263-0.6448-0.07770.4268-0.244-0.05440.3278-0.53950.21070.81610.00670.18420.5888-0.00390.830622.2967-122.700325.3721
93.5555-0.266-0.27230.88970.3881.8894-0.0541-0.5758-0.03670.92940.11430.6453-0.65640.3014-0.09020.77790.2560.07830.62070.00370.6692-31.0281-37.63451.8721
103.6581-0.5006-0.6762.0261-0.0462.35680.05070.006-0.1663-0.0092-0.00880.0120.2336-0.0227-0.03070.62340.09420.00980.41040.0480.5604-11.3711-59.853240.5538
111.4098-1.0539-1.59271.7190.73041.9232-0.14620.309-0.02690.1179-0.0008-0.13070.0572-0.04990.08030.50850.1516-0.06960.44320.08530.5076-15.3788-51.077641.2761
122.8639-1.55790.30112.404-0.03951.4601-0.1277-0.2932-0.49430.8407-0.10930.8417-0.0353-0.0654-0.0050.3710.31760.0320.69730.18290.6583-33.3565-46.996450.0991
133.1740.26110.13281.10050.3531.525-0.07410.21420.4395-0.2817-0.06150.0197-0.46660.11150.16680.68290.08020.00030.48160.14060.5633-15.4198-28.242340.8283
144.88340.87451.49561.6818-0.86431.65150.23010.73110.4395-0.6015-0.3832-0.2809-0.14540.29640.08610.7466-0.02710.0590.74450.00310.642-8.3211-26.263541.3527
152.212-0.64791.12863.00510.87933.28970.20310.5891-0.0401-0.5799-0.12630.2003-0.7780.3503-0.07980.9572-0.05220.2160.7630.17450.829-18.4896-81.052152.4093
163.60141.9054-0.40517.9596-1.84492.0424-0.16470.55280.38320.2915-0.61930.1350.0144-1.0920.77961.07480.15750.26950.86330.07680.9128-27.7008-85.745955.086
176.8241-0.7077-1.07196.53942.07447.2188-0.87210.9008-1.7877-0.4735-0.5814-0.64571.9906-0.41871.14221.48210.02280.45740.8226-0.03921.243-19.6388-91.936952.9864
183.68151.5854-0.39246.41360.20598.25140.23760.0013-0.12610.7930.149-1.08-0.21010.9287-0.13451.11960.15080.32590.85540.27061.0677-13.0914-83.509261.8766
194.4957-3.3744-2.45373.098-0.12138.1385-0.59440.286-0.6340.12660.8141-0.00190.69190.4686-0.27370.84840.04370.24341.00330.09641.105-6.9676-86.236351.2446
204.1267-1.407-1.21716.02821.49244.7730.04590.3962-1.0671-0.08790.90070.43150.6386-0.6061-0.79621.9083-0.19150.26461.30570.01351.2989-31.204-94.378750.9163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 420 )
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 456 )
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 518 )
7X-RAY DIFFRACTION7chain 'A' and (resid 519 through 646 )
8X-RAY DIFFRACTION8chain 'A' and (resid 647 through 764 )
9X-RAY DIFFRACTION9chain 'B' and (resid 346 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 707 )
11X-RAY DIFFRACTION11chain 'B' and (resid 708 through 780 )
12X-RAY DIFFRACTION12chain 'B' and (resid 781 through 839 )
13X-RAY DIFFRACTION13chain 'B' and (resid 840 through 1016 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1017 through 1093 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 29 )
16X-RAY DIFFRACTION16chain 'C' and (resid 30 through 50 )
17X-RAY DIFFRACTION17chain 'C' and (resid 51 through 80 )
18X-RAY DIFFRACTION18chain 'C' and (resid 81 through 112 )
19X-RAY DIFFRACTION19chain 'C' and (resid 113 through 149 )
20X-RAY DIFFRACTION20chain 'C' and (resid 150 through 157 )

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