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- PDB-1mg1: HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA -

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Basic information

Entry
Database: PDB / ID: 1mg1
TitleHTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA
ComponentsPROTEIN (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)
KeywordsVIRAL PROTEIN / HUMAN T CELL LEUKEMIA VIRUS TYPE 1 / HTLV-1 / ENVELOPE PROTEIN / MEMBRANE FUSION / MALTOSE-BINDING PROTEIN CHIMERA
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Helix Hairpins - #210 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Helix Hairpins / Orthogonal Bundle ...Helix Hairpins - #210 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Helix Hairpins / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKobe, B. / Center, R.J. / Kemp, B.E. / Poumbourios, P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins.
Authors: Kobe, B. / Center, R.J. / Kemp, B.E. / Poumbourios, P.
#1: Journal: Protein Sci. / Year: 1998
Title: Crystallization of a Trimeric Human T Cell Leukemia Virus Type 1 Gp21 Ectodomain Fragment as a Chimera with Maltose-Binding Protein
Authors: Center, R.J. / Kobe, B. / Wilson, K.A. / Teh, T. / Howlett, G.J. / Kemp, B.E. / Poumbourios, P.
History
DepositionMar 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7994
Polymers49,3861
Non-polymers4133
Water66737
1
A: PROTEIN (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)
hetero molecules

A: PROTEIN (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)
hetero molecules

A: PROTEIN (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,39812
Polymers148,1583
Non-polymers1,2409
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13630 Å2
ΔGint-103 kcal/mol
Surface area56060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.947, 102.947, 118.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-457-

CL

21A-458-

CL

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Components

#1: Protein PROTEIN (HTLV-1 GP21 ECTODOMAIN/MALTOSE-BINDING PROTEIN CHIMERA)


Mass: 49386.023 Da / Num. of mol.: 1 / Fragment: GP21 ECTODOMAIN (GP62 RESIDUES 338-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / Strain: 3-19-3 / Cellular location: VIRUS ENVELOPEViral envelope / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3/PLYSS) / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.7 / Details: pH 4.7
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2(NH4)2SO411
3SODIUM ACETATE11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
21
31

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→99 Å / Num. obs: 19248 / % possible obs: 91 % / Redundancy: 7.8 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.8
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.2 / % possible all: 65
Reflection
*PLUS
Num. measured all: 150336
Reflection shell
*PLUS
% possible obs: 65 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.5→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1036 6.8 %RANDOM
Rwork0.223 ---
all-15268 --
obs-15268 94.6 %-
Displacement parametersBiso mean: 65.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20.41 Å20 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-40 Å
Luzzati sigma a0.73 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 25 37 3545
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.541.5
X-RAY DIFFRACTIONx_mcangle_it4.052
X-RAY DIFFRACTIONx_scbond_it3.872
X-RAY DIFFRACTIONx_scangle_it5.882.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.451 105 7.1 %
Rwork0.44 1369 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2FE.PARWATCL.TOP
X-RAY DIFFRACTION3MAL.PROMAL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61
LS refinement shell
*PLUS
Rfactor obs: 0.44

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