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- PDB-3zlc: Crystal Structure of Erv41p -

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Basic information

Entry
Database: PDB / ID: 3zlc
TitleCrystal Structure of Erv41p
ComponentsER-DERIVED VESICLES PROTEIN ERV41
KeywordsPROTEIN TRANSPORT / EARLY SECRETORY PATHWAY / ENDOPLASMIC RETICULUM / COPII VESICLE
Function / homology
Function and homology information


retrograde transporter complex, Golgi to ER / COPII-coated ER to Golgi transport vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ER to Golgi transport vesicle membrane / protein transport / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Endoplasmic reticulum vesicle transporter, C-terminal / Endoplasmic reticulum vesicle transporter, N-terminal / Endoplasmic reticulum vesicle transporter / Endoplasmic reticulum vesicle transporter / Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
Similarity search - Domain/homology
ER-derived vesicles protein ERV41
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsBiterova, E.I. / Svard, M. / Possner, D.D.D. / Guy, J.E.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The Crystal Structure of the Lumenal Domain of Erv41P, a Protein Involved in Transport between the Endoplasmic Reticulum and Golgi Apparatus
Authors: Biterova, E.I. / Svard, M. / Possner, D.D.D. / Guy, J.E.
History
DepositionJan 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ER-DERIVED VESICLES PROTEIN ERV41
B: ER-DERIVED VESICLES PROTEIN ERV41


Theoretical massNumber of molelcules
Total (without water)58,2192
Polymers58,2192
Non-polymers00
Water4,324240
1
A: ER-DERIVED VESICLES PROTEIN ERV41


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ER-DERIVED VESICLES PROTEIN ERV41


Theoretical massNumber of molelcules
Total (without water)29,1101
Polymers29,1101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-10 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.785, 76.935, 65.116
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8662, 0.0747, 0.494), (0.0805, -0.9967, 0.0095), (0.4931, 0.0316, -0.8694)
Vector: 50.9395, 3.7477, 8.1015)

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Components

#1: Protein ER-DERIVED VESICLES PROTEIN ERV41 / ERV41P


Mass: 29109.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PFHMSP-N / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q04651
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 0.2 M NH4NO3, 16 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→48.14 Å / Num. obs: 31843 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.41
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.41 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→48.14 Å / SU ML: 0.16 / σ(F): 2 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1999 6.3 %
Rwork0.1648 --
obs0.1675 31839 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 1.999→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 0 240 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093725
X-RAY DIFFRACTIONf_angle_d1.2135077
X-RAY DIFFRACTIONf_dihedral_angle_d15.8551397
X-RAY DIFFRACTIONf_chiral_restr0.09561
X-RAY DIFFRACTIONf_plane_restr0.005666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0490.23261280.19181912X-RAY DIFFRACTION90
2.049-2.10440.22351410.17582111X-RAY DIFFRACTION98
2.1044-2.16640.22471450.16712159X-RAY DIFFRACTION100
2.1664-2.23630.22131440.15712148X-RAY DIFFRACTION100
2.2363-2.31620.19991420.16052122X-RAY DIFFRACTION100
2.3162-2.4090.20111450.16292162X-RAY DIFFRACTION100
2.409-2.51860.20981440.16642138X-RAY DIFFRACTION100
2.5186-2.65140.22721450.16642161X-RAY DIFFRACTION100
2.6514-2.81750.27681430.17752139X-RAY DIFFRACTION100
2.8175-3.0350.20121440.17522142X-RAY DIFFRACTION100
3.035-3.34030.20771440.16952162X-RAY DIFFRACTION100
3.3403-3.82350.18711460.14922167X-RAY DIFFRACTION99
3.8235-4.81650.17451430.14162148X-RAY DIFFRACTION99
4.8165-48.15370.20871450.18582169X-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)
11.93940.762-0.37182.1606-0.44061.6963-0.0308-0.0687-0.12370.00870.08350.01120.1454-0.0827-0.02680.1280.0080.0010.13450.01540.121845.8396-13.477325.3734
21.4167-1.12610.79292.6492-0.93691.4663-0.01760.1010.0643-0.05030.0387-0.06-0.1320.0088-0.02530.1493-0.01970.0290.1620.00180.113950.40094.32048.3232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 51 THROUGH 293 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 51 THROUGH 294 )

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