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- PDB-1z9o: 1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Doma... -

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Basic information

Entry
Database: PDB / ID: 1z9o
Title1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the Rat ORP1 FFAT Motif
Components
  • Oxysterol binding protein
  • Vesicle-associated membrane protein-associated protein A
KeywordsPROTEIN BINDING/LIPID BINDING PROTEIN / VAP-33 / VAP-A / VAP-B / VAP-C / VAPA / VAPB / VAPC / VAP-33a / Scs2 / ERG30 / FFAT motif / ER / endoplasmic reticulum / targeting / immunoglobulin-like beta sheet / MSP homology domain / OSBP / ORP / oxysterol binding protein / PROTEIN BINDING-LIPID BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / organelle membrane contact site / ceramide transport / COPII-coated vesicle budding / MHC class II antigen presentation / positive regulation by host of viral genome replication / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...Synthesis of bile acids and bile salts / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / organelle membrane contact site / ceramide transport / COPII-coated vesicle budding / MHC class II antigen presentation / positive regulation by host of viral genome replication / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation by host of viral genome replication / sterol transport / perinuclear endoplasmic reticulum / protein localization to endoplasmic reticulum / phospholipid transport / cholesterol transport / Neutrophil degranulation / cholesterol binding / lipid transport / viral release from host cell / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-membrane adaptor activity / neuron projection development / late endosome / microtubule cytoskeleton / microtubule binding / nuclear membrane / vesicle / endosome / protein domain specific binding / protein heterodimerization activity / Golgi membrane / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PapD-like superfamily ...Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PapD-like superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Oxysterol-binding protein-related protein 1 / Vesicle-associated membrane protein-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T.
CitationJournal: Structure / Year: 2005
Title: Structural basis of FFAT motif-mediated ER targeting
Authors: Kaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T.
History
DepositionApr 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein A
B: Vesicle-associated membrane protein-associated protein A
C: Vesicle-associated membrane protein-associated protein A
D: Vesicle-associated membrane protein-associated protein A
E: Vesicle-associated membrane protein-associated protein A
F: Vesicle-associated membrane protein-associated protein A
G: Oxysterol binding protein
H: Oxysterol binding protein
I: Oxysterol binding protein
J: Oxysterol binding protein
K: Oxysterol binding protein
L: Oxysterol binding protein


Theoretical massNumber of molelcules
Total (without water)94,32612
Polymers94,32612
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.048, 50.033, 90.287
Angle α, β, γ (deg.)90.01, 90.00, 60.03
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12G
22L

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA5 - 1258 - 128
21METMETFF5 - 1258 - 128
12SERSERGG473 - 4812 - 10
22SERSERLL473 - 4812 - 10

NCS ensembles :
ID
1
2

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Components

#1: Protein
Vesicle-associated membrane protein-associated protein A / VAMP- associated protein A / VAMP-A / VAP-A / 33 kDa Vamp-associated protein / VAP-33


Mass: 14545.880 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vapa, Vap33 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 61889097, UniProt: Q9Z270*PLUS
#2: Protein/peptide
Oxysterol binding protein / ORP-1


Mass: 1175.157 Da / Num. of mol.: 6 / Fragment: Residues 472-481 / Source method: obtained synthetically
Details: peptide NH2-SEDEFYDALS-COO corresponding to rat ORP1 472-481 synthesized by Biopeptide LLC
References: UniProt: Q8K4M9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 2000 MME, sodium thiocyanate, tris buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111.03311.0331
SYNCHROTRONALS 8.2.120.97940.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDAug 28, 2004
ADSC QUANTUM 42CCDAug 28, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03311
20.97941
ReflectionResolution: 1.9→50 Å / Num. all: 59859 / Num. obs: 59506 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 %
Reflection shellResolution: 1.9→1.949 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: Found Se by molecular replacement w/ 1Z9L

1z9l


Resolution: 1.9→14.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.431 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26051 6029 10.1 %RANDOM
Rwork0.21472 ---
obs0.21941 53477 100 %-
all-53477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.342 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0.45 Å20.05 Å2
2--1 Å2-0.02 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 0 185 6329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0226240
X-RAY DIFFRACTIONr_bond_other_d0.0020.025664
X-RAY DIFFRACTIONr_angle_refined_deg2.4921.9878442
X-RAY DIFFRACTIONr_angle_other_deg1.135313320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4524.651258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.326151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0941530
X-RAY DIFFRACTIONr_chiral_restr0.1530.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined0.1920.21005
X-RAY DIFFRACTIONr_nbd_other0.2150.25600
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22768
X-RAY DIFFRACTIONr_nbtor_other0.1020.23860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1070.27
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7861.54793
X-RAY DIFFRACTIONr_mcbond_other0.5041.51518
X-RAY DIFFRACTIONr_mcangle_it2.09326378
X-RAY DIFFRACTIONr_scbond_it3.46632670
X-RAY DIFFRACTIONr_scangle_it4.6134.52064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1849tight positional0.030.05
2G111tight positional0.030.05
1A1849tight thermal0.170.5
2G111tight thermal0.220.5
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 457 -
Rwork0.266 3925 -
obs--100 %
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)
12.42191.19980.05096.64931.31278.44670.2008-0.23010.1329-0.1189-0.0435-0.19850.10331.1198-0.1573-0.32290.01190.03320.0252-0.0696-0.1735-13.40443.77183.15
26.509-1.19151.02652.3591-0.58548.4439-0.14690.1143-0.0878-0.02970.28390.22081.0113-0.4263-0.137-0.052-0.1386-0.046-0.25490.0613-0.1697-31.1533.5396.534
34.30612.4073-1.15324.5083-0.47418.5360.146-0.160.2205-0.26520.014-0.04-0.9331-0.6866-0.16-0.07880.15540.0704-0.23440.0039-0.1744-30.48153.63366.441
44.1257-2.24951.01134.6758-0.54998.62150.16050.2101-0.23170.2915-0.0017-0.0260.9444-0.6865-0.1587-0.0709-0.1572-0.0789-0.23380.0071-0.1664-30.46533.14253.05
56.30820.9737-1.00012.3218-0.61488.5598-0.1335-0.1140.082-0.00750.30560.1993-1.0279-0.4717-0.1721-0.0650.1430.0419-0.25240.0636-0.1695-31.16753.222113.244
62.4622-1.2828-0.01726.29981.22578.58320.24560.2304-0.14080.1217-0.0969-0.1656-0.13871.1281-0.1487-0.3261-0.012-0.03480.0203-0.0639-0.1727-13.41442.979126.621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1258 - 128
2X-RAY DIFFRACTION1GG473 - 4812 - 10
3X-RAY DIFFRACTION2BB5 - 1258 - 128
4X-RAY DIFFRACTION2HH473 - 4812 - 10
5X-RAY DIFFRACTION3CC5 - 1258 - 128
6X-RAY DIFFRACTION3II473 - 4812 - 10
7X-RAY DIFFRACTION4DD5 - 1258 - 128
8X-RAY DIFFRACTION4JJ473 - 4812 - 10
9X-RAY DIFFRACTION5EE5 - 1258 - 128
10X-RAY DIFFRACTION5KK473 - 4812 - 10
11X-RAY DIFFRACTION6FF5 - 1258 - 128
12X-RAY DIFFRACTION6LL473 - 4812 - 10

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