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Basic information

Entry
Database: PDB / ID: 4oqt
TitleLINGO-1/Li81 Fab complex
Components
  • Heavy Chain of Li81 Fab, VH3-23
  • Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
  • Light Chain of Li81 Fab, kappa 3
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / Leucine rich repeat / Ig domain / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Axonal growth inhibition (RHOA activation) / immunoglobulin complex / epidermal growth factor receptor binding / extracellular matrix / immune response / extracellular space / plasma membrane
Similarity search - Function
Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain ...Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Leucine-rich repeat domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IGK@ protein / Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1 / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsPepinsky, R.B. / Arndt, J.W. / Quan, C. / Gao, Y. / Quintero-Monzon, O. / Lee, X. / Mi, S.
CitationJournal: J.Pharmacol.Exp.Ther. / Year: 2014
Title: Structure of the LINGO-1-Anti-LINGO-1 Li81 Antibody Complex Provides Insights into the Biology of LINGO-1 and the Mechanism of Action of the Antibody Therapy.
Authors: Pepinsky, R.B. / Arndt, J.W. / Quan, C. / Gao, Y. / Quintero-Monzon, O. / Lee, X. / Mi, S.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
L: Light Chain of Li81 Fab, kappa 3
H: Heavy Chain of Li81 Fab, VH3-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,88610
Polymers102,8353
Non-polymers3,0517
Water0
1
A: Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
L: Light Chain of Li81 Fab, kappa 3
H: Heavy Chain of Li81 Fab, VH3-23
hetero molecules

A: Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
L: Light Chain of Li81 Fab, kappa 3
H: Heavy Chain of Li81 Fab, VH3-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,77220
Polymers205,6716
Non-polymers6,10214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
2
A: Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
hetero molecules

L: Light Chain of Li81 Fab, kappa 3
H: Heavy Chain of Li81 Fab, VH3-23


Theoretical massNumber of molelcules
Total (without water)105,88610
Polymers102,8353
Non-polymers3,0517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
Buried area8250 Å2
ΔGint26 kcal/mol
Surface area41860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.470, 207.470, 140.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1 / Leucine-rich repeat and immunoglobulin domain-containing protein 1 / Leucine-rich repeat neuronal ...Leucine-rich repeat and immunoglobulin domain-containing protein 1 / Leucine-rich repeat neuronal protein 1 / Leucine-rich repeat neuronal protein 6A


Mass: 54436.477 Da / Num. of mol.: 1 / Fragment: UNP residues 40-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LINGO1, LERN1, LRRN6A, UNQ201/PRO227 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q96FE5

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Antibody , 2 types, 2 molecules LH

#2: Antibody Light Chain of Li81 Fab, kappa 3


Mass: 23650.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6PIL8*PLUS
#3: Antibody Heavy Chain of Li81 Fab, VH3-23


Mass: 24748.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: S6B291*PLUS

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Sugars , 3 types, 7 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 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: 4.26 Å3/Da / Density % sol: 71.14 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 36% pentaerythritol propoxylate (5/4 PO/OH), 0.2M sodium thiocyanate, 0.1M HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.23→20 Å / Num. obs: 27561 / % possible obs: 99.43 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.23→3.4 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 44.177 / SU ML: 0.339 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1479 5.1 %RANDOM
Rwork0.192 ---
obs0.195 27561 99.4 %-
all-27561 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.65 Å2-0 Å2
2--1.31 Å20 Å2
3----4.24 Å2
Refinement stepCycle: LAST / Resolution: 3.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 201 0 7257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197475
X-RAY DIFFRACTIONr_bond_other_d0.0010.026937
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.99810203
X-RAY DIFFRACTIONr_angle_other_deg0.859315883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7945907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10923.699319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.635151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4251550
X-RAY DIFFRACTIONr_chiral_restr0.0920.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021701
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_it3.8456.9073637
X-RAY DIFFRACTIONr_mcbond_other3.8456.9063636
X-RAY DIFFRACTIONr_mcangle_it5.98510.3624541
X-RAY DIFFRACTIONr_mcangle_other5.98510.3634542
X-RAY DIFFRACTIONr_scbond_it4.8827.5033838
X-RAY DIFFRACTIONr_scbond_other4.8757.5033838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.53811.125663
X-RAY DIFFRACTIONr_long_range_B_refined9.53355.5837811
X-RAY DIFFRACTIONr_long_range_B_other9.53255.5887812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.23→3.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 98 -
Rwork0.289 2002 -
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)
12.09850.66571.16481.3441-0.13722.25060.057-0.28790.01890.144-0.1706-0.0582-0.4955-0.07530.11360.2057-0.05840.01280.0682-0.03290.073568.847258.622514.2665
22.4015-2.7412-2.81198.03184.91337.2683-0.0276-0.00510.07160.1304-0.0658-0.0032-0.0074-0.16620.09340.0283-0.058-0.05250.18620.08910.133848.930541.6659-32.0057
32.22350.45362.914.0299-1.18987.63550.1980.32090.00080.0952-0.1419-0.41730.18320.7143-0.05610.07820.0329-0.07350.4064-0.0050.353388.67429.36538.1749
42.00121.30760.71326.31321.43652.5223-0.1049-0.0458-0.11860.38010.143-0.519-0.13530.4529-0.03820.2857-0.0881-0.13960.22250.01680.151486.8954-1.101347.162
52.49582.1887-0.36276.4275-2.45572.9501-0.1283-0.3574-0.1474-0.08970.0262-0.15690.36770.02450.10210.09870.05390.05470.11420.03180.090667.577223.441531.1516
65.1861-0.41512.99714.2361-2.50536.0487-0.0308-0.4948-0.01540.59030.23270.17050.0003-0.1891-0.20190.4214-0.04850.04010.1034-0.01850.133272.7231-4.289254.5019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 381
2X-RAY DIFFRACTION2A382 - 477
3X-RAY DIFFRACTION3H1 - 117
4X-RAY DIFFRACTION4H118 - 221
5X-RAY DIFFRACTION5L1 - 110
6X-RAY DIFFRACTION6L111 - 214

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