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- PDB-6p57: Crystal Structure of the Beta Subunit of Luteinizing Hormone -

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Basic information

Entry
Database: PDB / ID: 6p57
TitleCrystal Structure of the Beta Subunit of Luteinizing Hormone
ComponentsLutropin subunit beta
KeywordsHORMONE / reproduction / glycosylation / gonadotropic hormone / cysteine knot
Function / homology
Function and homology information


Mineralocorticoid biosynthesis / Glycoprotein hormones / Hormone ligand-binding receptors / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Reactions specific to the complex N-glycan synthesis pathway / hormone-mediated signaling pathway / hormone activity / G protein-coupled receptor signaling pathway / extracellular space / cytoplasm
Similarity search - Function
Gonadotropin, beta subunit, conserved site / Glycoprotein hormones beta chain signature 1. / Glycoprotein hormones beta chain signature 2. / Glycoprotein hormone beta chain homologues. / Gonadotropin, beta subunit / Glycoprotein hormone subunit beta / Cystine-knot domain / Cystine-knot cytokine
Similarity search - Domain/homology
alpha-D-mannopyranose / Lutropin subunit beta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsMcPherson, A.
CitationJournal: Curr Res Struct Biol / Year: 2019
Title: The Crystal Structure of the Beta Subunit of Luteinizing Hormone and a Model for the Intact Hormone
Authors: Larson, S.B. / McPherson, A.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lutropin subunit beta
B: Lutropin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0267
Polymers30,4302
Non-polymers2,5965
Water41423
1
A: Lutropin subunit beta
hetero molecules

A: Lutropin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2566
Polymers30,4302
Non-polymers1,8264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_655-x+3/2,-y+1/2,z1
Buried area4120 Å2
ΔGint19 kcal/mol
Surface area14960 Å2
MethodPISA
2
B: Lutropin subunit beta
hetero molecules

B: Lutropin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7968
Polymers30,4302
Non-polymers3,3666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4470 Å2
ΔGint30 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.016, 80.016, 206.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein / Non-polymers , 2 types, 25 molecules AB

#1: Protein Lutropin subunit beta / Luteinizing hormone subunit beta / LSH-beta / Lutropin beta chain


Mass: 15215.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04651
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3-1-4/a4-b1_a6-f1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 2.79 Å3/Da / Density % sol: 56 % / Description: thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop with the drop composed of equal quantities of 20 mg/ml protein dissolved in water, and 20% PEG 3350 plus 1% beta octyl glucoside dissolved in 0.10 M MES buffer at pH 6.5. Room ...Details: Sitting drop with the drop composed of equal quantities of 20 mg/ml protein dissolved in water, and 20% PEG 3350 plus 1% beta octyl glucoside dissolved in 0.10 M MES buffer at pH 6.5. Room temperature crystallization.
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X7B / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. obs: 6465 / % possible obs: 98.43 % / Redundancy: 9.35 % / Biso Wilson estimate: 85 Å2 / CC1/2: 0.89 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.16 / Rsym value: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.15 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 480 / CC1/2: 0.34 / Rrim(I) all: 0.68 / Rsym value: 0.6 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HCN

1hcn


Resolution: 3.16→33.32 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.83 / SU B: 11.107 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28605 289 5 %RANDOM
Rwork0.20716 ---
obs0.21095 5482 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 146.762 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.84 Å2
Refinement stepCycle: 1 / Resolution: 3.16→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 174 23 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191922
X-RAY DIFFRACTIONr_bond_other_d0.0020.021807
X-RAY DIFFRACTIONr_angle_refined_deg1.8042.1122650
X-RAY DIFFRACTIONr_angle_other_deg0.99934253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.27621.13253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.6281516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0221904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7077.909898
X-RAY DIFFRACTIONr_mcbond_other5.7097.903897
X-RAY DIFFRACTIONr_mcangle_it9.2098.8731116
X-RAY DIFFRACTIONr_mcangle_other9.2058.8781117
X-RAY DIFFRACTIONr_scbond_it5.1088.2581023
X-RAY DIFFRACTIONr_scbond_other5.0988.2591023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9069.2631531
X-RAY DIFFRACTIONr_long_range_B_refined18.073186530
X-RAY DIFFRACTIONr_long_range_B_other18.074186529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.161→3.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 19 -
Rwork0.133 384 -
obs--97.58 %
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)
11.7088-0.5281-0.74751.8737-1.20073.14930.3533-0.0270.25460.14730.01350.1196-0.5389-0.0764-0.36680.2411-0.09460.09570.1098-0.03280.116747.294925.164877.6267
24.5494-2.7497-1.65932.8888-0.76063.95760.06720.12550.5652-0.03290.2404-0.1094-0.4122-0.3632-0.30760.2467-0.1316-0.05790.18060.07440.201536.142413.539879.8246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 111
2X-RAY DIFFRACTION2B1 - 118

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