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- PDB-2id5: Crystal Structure of the Lingo-1 Ectodomain -

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Basic information

Entry
Database: PDB / ID: 2id5
TitleCrystal Structure of the Lingo-1 Ectodomain
ComponentsLeucine rich repeat neuronal 6A
KeywordsLIGAND BINDING PROTEIN / MEMBRANE PROTEIN / CNS-specific LRR-Ig containing
Function / homology
Function and homology information


Axonal growth inhibition (RHOA activation) / epidermal growth factor receptor binding / extracellular matrix / 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 / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / 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
Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.698 Å
AuthorsMosyak, L. / Wood, A. / Dwyer, B. / Johnson, M. / Stahl, M.L. / Somers, W.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The structure of the Lingo-1 ectodomain, a module implicated in central nervous system repair inhibition.
Authors: Mosyak, L. / Wood, A. / Dwyer, B. / Buddha, M. / Johnson, M. / Aulabaugh, A. / Zhong, X. / Presman, E. / Benard, S. / Kelleher, K. / Wilhelm, J. / Stahl, M.L. / Kriz, R. / Gao, Y. / Cao, Z. ...Authors: Mosyak, L. / Wood, A. / Dwyer, B. / Buddha, M. / Johnson, M. / Aulabaugh, A. / Zhong, X. / Presman, E. / Benard, S. / Kelleher, K. / Wilhelm, J. / Stahl, M.L. / Kriz, R. / Gao, Y. / Cao, Z. / Ling, H.P. / Pangalos, M.N. / Walsh, F.S. / Somers, W.S.
History
DepositionSep 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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_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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _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_atom_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 neuronal 6A
B: Leucine rich repeat neuronal 6A
C: Leucine rich repeat neuronal 6A
D: Leucine rich repeat neuronal 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,59430
Polymers217,0934
Non-polymers10,50126
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.517, 149.720, 157.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Non-polymers , 2 types, 312 molecules ABCD

#1: Protein
Leucine rich repeat neuronal 6A / Lingo-1


Mass: 54273.305 Da / Num. of mol.: 4 / Fragment: Extracelullar portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRN6A / Plasmid: pSMEG / Cell (production host): Hampster Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1 / References: UniProt: Q96FE5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 26 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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
#3: 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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-L-Gulp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.4 M Am Sulfate, O.1 M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.698→158.11 Å / Num. all: 122982 / Num. obs: 122982 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.09 / Net I/σ(I): 61
Reflection shellResolution: 2.698→2.8 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.61 / % possible all: 94.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.698→158.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.053 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6536 5 %RANDOM
Rwork0.214 ---
all0.216 129519 --
obs0.216 122982 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.945 Å2
Baniso -1Baniso -2Baniso -3
1--4.45 Å20 Å20 Å2
2--6.26 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.698→158.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15122 0 689 308 16119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216208
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.0222091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11251879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09223.226744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12152644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81315142
X-RAY DIFFRACTIONr_chiral_restr0.0780.22638
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211882
X-RAY DIFFRACTIONr_nbd_refined0.1990.26258
X-RAY DIFFRACTIONr_nbtor_refined0.320.210832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2464
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.24
X-RAY DIFFRACTIONr_mcbond_it0.4181.59658
X-RAY DIFFRACTIONr_mcangle_it0.736215273
X-RAY DIFFRACTIONr_scbond_it1.16837166
X-RAY DIFFRACTIONr_scangle_it2.0024.56817
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 453 -
Rwork0.326 8340 -
obs-8793 91.28 %
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)
11.3414-0.41460.5080.394-0.93214.7878-0.0446-0.0171-0.00880.1195-0.01640.0867-0.1964-0.07920.0611-0.24520.01140.0172-0.44350.0264-0.192757.241423.951836.9308
25.52441.3662-0.04840.80730.04661.12690.01820.35620.4417-0.00480.03610.1373-0.16540.0417-0.0544-0.25140.0174-0.0214-0.37710.082-0.269298.663629.3372-1.1511
30.08060.0416-0.02680.2623-0.02385.3873-0.0224-0.0840.13280.04110.0011-0.0826-0.34030.30720.0212-0.2463-0.1333-0.07110.0725-0.0307-0.1703138.783632.364640.8687
48.1310.36121.68430.60880.18242.7999-0.0109-1.08861.04070.1689-0.14830.0914-0.3675-0.56010.1592-0.0640.04250.0576-0.0898-0.2073-0.150297.452329.009978.5326
57.3834-6.46994.261717.4657-4.58864.27190.1667-0.3324-1.13041.23170.3516-0.11780.26970.0676-0.51820.16990.0139-0.03850.1802-0.00950.13372.71991.455285.2178
64.42362.3444-1.080714.4477-4.66483.96890.008-0.0826-0.62760.0087-0.04420.97760.8922-0.07630.03620.1996-0.0190.17760.0337-0.14570.153953.8362-0.58468.4563
76.22117.80752.3323.69794.71634.272-0.12560.1336-0.9646-1.30880.159-0.11660.27810.0829-0.03340.00370.0968-0.0299-0.04190.10390.03127.67296.416-7.471
83.2582-2.8742-0.78910.06753.47412.428-0.07430.1495-0.62490.46350.1327-0.54310.67510.0489-0.05840.1051-0.0673-0.03920.1976-0.01720.1026147.28338.289968.7305
92.22180.1647-0.10581.99710.06556.2769-0.02230.7210.1338-0.09130.07240.5818-0.1347-0.7349-0.05010.00120.0010.0010.0014-0.00130.001659.245620.304546.5831
104.87321.4884-1.06692.2693-0.23152.6394-0.19610.44980.9652-0.3750.3866-0.1954-0.45560.3003-0.19050.00140.0021-0.00160.0017-0.00520.002589.996326.87570.5756
113.24120.020.26511.6211.40664.8939-0.0744-0.67090.29860.04270.3125-0.4769-0.51920.4127-0.23820.0011-0.0002-0.00080.0002-0.00170.0004136.390630.386530.7429
125.4328-1.5818-0.90922.71180.71543.9706-0.0844-0.75321.16010.34160.50340.1899-0.7193-0.7712-0.41890.00080.0001-0.00010.00120.00160.0005107.633928.832974.3567
130.1135-0.00390.01830.0133-0.02270.18490.0167-0.0690.0977-0.0124-0.0120.0334-0.03310.031-0.00470.07770.03010.0205-0.4339-0.02630.001196.939223.92431.8379
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 3821 - 382
22BB3 - 3823 - 382
33CC2 - 3822 - 382
44DD3 - 3823 - 382
55AA383 - 477383 - 477
66BB383 - 475383 - 475
77CC383 - 477383 - 477
88DD383 - 476383 - 476
99AH - K485 - 4911
1010BO - Q486 - 4881
1111CV - X485 - 4871
1212DDA - AA487 - 4832
1313C - AGA - EA491 - 5721 - 81

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