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- PDB-1lsh: LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN -

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Basic information

Entry
Database: PDB / ID: 1lsh
TitleLIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN
Components
  • LIPOVITELLIN (LV-1N, LV-1C)
  • LIPOVITELLIN (LV-2)
KeywordsLIPID BINDING PROTEIN / LIPOVITELLIN / VITELLOGENIN / LIPOPROTEIN / PLASMA APOLIPOPROTE APOLIPOPROTEIN B / APOB / MICROSOMAL TRIGLYCERIDE TRANSFER PR BOUNDARY LIPID / PHOSPHOLIPID STRUCTURE
Function / homology
Function and homology information


nutrient reservoir activity / lipid transporter activity / cellular response to estrogen stimulus / response to estradiol
Similarity search - Function
Vitellinogen, superhelical / Outer Surface Protein A; domain 2 / Lipovitellin. Chain A, domain 3 / Lipovitellin-phosvitin complex, chain A, domain 4 / Lipovitellin-phosvitin complex, chain A, domain 4 / Lipovitellin-phosvitin complex; beta-sheet shell regions / Vitellinogen, beta-sheet shell domain / Vitellinogen, beta-sheet shell / Vitellinogen, beta-sheet shell domain superfamily / Vitellinogen, beta-sheet shell ...Vitellinogen, superhelical / Outer Surface Protein A; domain 2 / Lipovitellin. Chain A, domain 3 / Lipovitellin-phosvitin complex, chain A, domain 4 / Lipovitellin-phosvitin complex, chain A, domain 4 / Lipovitellin-phosvitin complex; beta-sheet shell regions / Vitellinogen, beta-sheet shell domain / Vitellinogen, beta-sheet shell / Vitellinogen, beta-sheet shell domain superfamily / Vitellinogen, beta-sheet shell / DUF1944 / Lipovitellin-phosvitin complex; beta-sheet shell regions / Lipovitellin; beta-sheet shell regions, chain A / : / Vitellinogen, open beta-sheet, subdomain 1 / Vitellinogen, open beta-sheet / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Leucine-rich Repeat Variant / Single Sheet / Alpha Horseshoe / Roll / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
di-heneicosanoyl phosphatidyl choline / UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / Vitellogenin
Similarity search - Component
Biological speciesIchthyomyzon unicuspis (silver lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsThompson, J.R. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 2002
Title: Lipid-protein interactions in lipovitellin.
Authors: Thompson, J.R. / Banaszak, L.J.
#1: Journal: Structure / Year: 1998
Title: The Structural Basis of Lipid Interactions in Lipovitellin, a Souble Lipoprotein
Authors: Anderson, T.A. / Levitt, D.G. / Banaszak, L.J.
History
DepositionMay 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence / Refinement description
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / software / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Aug 18, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 99The disulfide bond S-S involving residues 156 and 182 in chain A is formed between the alternate ...The disulfide bond S-S involving residues 156 and 182 in chain A is formed between the alternate conformers B of these residues.
Remark 600HETEROGEN DUE TO LACK OF ELECTRON DENSITY, ONLY VARYING PARTS OF PHOSPHOLIPID MOLECULES COULD BE ...HETEROGEN DUE TO LACK OF ELECTRON DENSITY, ONLY VARYING PARTS OF PHOSPHOLIPID MOLECULES COULD BE MODELED. THE FIRST SEVEN MOLECULES WERE MODELED AS PHOSPHATIDYLCHOLINE WITH AN ALTERNATE CONFORMATION FOR ONE OF THE ACYL CHAINS IN MOLECULES 1 AND 5. MOLECULES 2-7 WERE MODELED AS UNKNOWN PHOSPHOLIPID BUT ARBITARILY CALLED PHOSPHATIDYLCHOLINE. ADDITIONAL 43 METHYLENE CHAIN FRAGMENTS WITH BETWEEN 20 AND 5 CARBON ATOMS EACH WERE MODELED. THREE OF THE HYDROCARBON SEGMENTS ARE BRANCHED BUT NOT MODELED AS PHOSPHOLIPID BECAUSE IT WAS IMPOSSIBLE TO IDENTIFY WHICH PORTION OF ELECTRON DENSITY BELONGED TO THE ACYL CHAINS AND POLAR HEADGROUPS. THE 43 MOLECULES NAMED UPL (ARBITARILY CALLED UNKNOWN BRANCHED PHOSPHOLIPID FRAGMENT) WAS SIMPLY MEANT TO REPRESENTS METHYLENE CHAIN FRAGMENTS.
Remark 999SEQUENCE LIPOVITELLIN IS PROTEOLYTICALLY PROCESSED FROM ITS PRECURSOR PRODUCING FOUR POLYPEPTIDES. ...SEQUENCE LIPOVITELLIN IS PROTEOLYTICALLY PROCESSED FROM ITS PRECURSOR PRODUCING FOUR POLYPEPTIDES. PRECISE CLEAVED LENGTHS OF FRAGMENTS LV-1N, LV-1C AND LV-2 ARE NOT KNOWN. BOTH LV-1N AND LV-1C ARE PRESENTED HERE AS SINGLE ENTITY WITH CHAIN A TO CORRESSPOND WITH HOMOGENEOUS SINGLE POLYPEPTIDE IN LIPOVITELLINS OF OTHER SPECIES. ONE OF THE FRAGMENTS, PHOVITIN CONSISTING OF 232 RESIDUES (1074-1305) IN THE SWS ENTRY WAS PRESENT IN THE CRYSTAL BUT NONE OF ITS RESIDUE COULD BE MODELED DUE TO LACK OF ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOVITELLIN (LV-1N, LV-1C)
B: LIPOVITELLIN (LV-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,30052
Polymers152,5802
Non-polymers26,72150
Water20,2131122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.170, 84.520, 89.530
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer believed to be generated by the crystallographic c2 dyad -x,y,-z

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Components

#1: Protein LIPOVITELLIN (LV-1N, LV-1C)


Mass: 117469.508 Da / Num. of mol.: 1 / Fragment: LV1n, LV1c / Source method: isolated from a natural source / Details: Egg Yolk / Source: (natural) Ichthyomyzon unicuspis (silver lamprey) / References: UniProt: Q91062
#2: Protein LIPOVITELLIN (LV-2)


Mass: 35110.094 Da / Num. of mol.: 1 / Fragment: LV2 / Source method: isolated from a natural source / Details: Egg Yolk / Source: (natural) Ichthyomyzon unicuspis (silver lamprey) / References: UniProt: Q91062
#3: Chemical
ChemComp-PLD / di-heneicosanoyl phosphatidyl choline


Mass: 875.313 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C50H101NO8P
#4: Chemical...
ChemComp-UPL / UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / UNKNOWN PHOSPHOLIPID FRAGMENT


Mass: 478.920 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C34H70
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Protein stock:10 mg/ml lipovitellin, 0.25 mM sodium citrate; Well: 0.55-0.61 M sodium citrate, 1mM thioglycerol, 1 mM EDTA, 0.05% sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.25 Msodium citrate1droppH6.2
30.55-0.61 Msodium citrate1reservoirpH6.2
41 mMthioglycerol1reservoir
51 mMEDTA1reservoir
60.05 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 7, 1998 / Details: vertically focusing mirror
RadiationMonochromator: double crystal Si220 monochromator,double crystal Si111 monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 82007 / Num. obs: 82007 / % possible obs: 74.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.54 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→1.99 Å / % possible all: 30.1
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: LIPOVITELLIN (ROOM TEMP)

Resolution: 1.9→21.6 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used OUTIER program (Randy Read) to reject 312 reflections in the range 30-5.9 Angstrom
RfactorNum. reflection% reflectionSelection details
Rfree0.255 983 1.2 %RANDOM
Rwork0.193 ---
all0.193 81695 --
obs0.193 81695 74.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 180.794 Å2 / ksol: 0.383954 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å2-3.79 Å2
2--5.26 Å20 Å2
3----2.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→21.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9156 0 657 1122 10935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d2.45
X-RAY DIFFRACTIONc_mcbond_it4.761.5
X-RAY DIFFRACTIONc_mcangle_it6.022
X-RAY DIFFRACTIONc_scbond_it7.042
X-RAY DIFFRACTIONc_scangle_it92.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.375 27 0.7 %
Rwork0.299 4076 -
obs-4076 30.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1LV_PROTEIN.PARLV_PROTEIN.TOP
X-RAY DIFFRACTION2LV_LIGAND.PARLV_LIGAND.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Version: 0.9,1.0,1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.45

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