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- PDB-3oja: Crystal structure of LRIM1/APL1C complex -

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Basic information

Entry
Database: PDB / ID: 3oja
TitleCrystal structure of LRIM1/APL1C complex
Components
  • Anopheles Plasmodium-responsive Leucine-rich repeat protein 1
  • Leucine-rich Immune Molecule 1
KeywordsPROTEIN BINDING / coiled-coil / helix-loop-helix / leucine-rich repeat
Function / homology
Function and homology information


defense response to symbiont / protein stabilization / extracellular space
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #140 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4090 / : / Dimerization domain in LRIM1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #140 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4090 / : / Dimerization domain in LRIM1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Leucine-rich repeat domain superfamily / Special / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsBaxter, R.H.G. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae.
Authors: Baxter, R.H. / Steinert, S. / Chelliah, Y. / Volohonsky, G. / Levashina, E.A. / Deisenhofer, J.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / pdbx_validate_close_contact / 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_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 Immune Molecule 1
B: Anopheles Plasmodium-responsive Leucine-rich repeat protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5009
Polymers124,2872
Non-polymers3,2137
Water11,043613
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-3 kcal/mol
Surface area51920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.890, 110.890, 168.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Leucine-rich Immune Molecule 1


Mass: 55097.066 Da / Num. of mol.: 1 / Fragment: UNP residues 23-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: AGAP006348, LRIM1 / Plasmid: Bac-to-Bac / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7Q5N3
#2: Protein Anopheles Plasmodium-responsive Leucine-rich repeat protein 1


Mass: 69190.023 Da / Num. of mol.: 1 / Fragment: UNP residues 140-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: AGAP007033, APL1C / Plasmid: Bac-to-Bac / Production host: Trichoplusia ni (cabbage looper)

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Sugars , 3 types, 7 molecules

#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.: 4
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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+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.: 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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Non-polymers , 1 types, 613 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 4.4 Å3/Da / Density % sol: 71.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG 1000, 0.1M NaCl, 50 mM Na-Hepes, pH 7.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 56906 / Num. obs: 56906 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.834 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.770.7152.117338417099.7
2.77-2.850.5872.516856404799.7
2.85-2.930.4842.916449394899.7
2.93-3.020.4273.316093386099.8
3.02-3.120.34415514372499.8
3.12-3.230.263514915359799.7
3.23-3.350.216614365348299.8
3.35-3.490.1737.213915336899.7
3.49-3.640.1388.613360323299.8
3.64-3.820.1219.712659309099.7
3.82-4.020.10810.612093294499.6
4.02-4.270.111.411393279699.5
4.27-4.560.09711.910712261799.4
4.56-4.930.09212.49866243399.1
4.93-5.40.09911.89140226199.2
5.4-6.040.1110.68287205298.7
6.04-6.970.103117187182898.5
6.97-8.540.08313.26071154798.1
8.54-12.070.06915.74821122197.8
12.07-500.06316.5255168992.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.23 Å
Translation3 Å49.23 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.56 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 2880 5.07 %RANDOM
Rwork0.2051 ---
all0.2082 57165 --
obs0.2082 56839 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.161 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 116.87 Å2 / Biso mean: 37.5566 Å2 / Biso min: 4.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.6008 Å20 Å20 Å2
2---0.0764 Å2-0 Å2
3---0.6772 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8203 0 212 613 9028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416940
X-RAY DIFFRACTIONf_angle_d1.34730524
X-RAY DIFFRACTIONf_chiral_restr0.11369
X-RAY DIFFRACTIONf_plane_restr0.0062612
X-RAY DIFFRACTIONf_dihedral_angle_d20.0364456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.74440.31461150.228625602675100
2.7444-2.79170.31921340.221125412675100
2.7917-2.84240.30391450.223525552700100
2.8424-2.89710.26651370.210225252662100
2.8971-2.95620.28171320.227825482680100
2.9562-3.02050.31751450.221325432688100
3.0205-3.09070.28151370.214725442681100
3.0907-3.1680.29881090.204625782687100
3.168-3.25360.29331400.204325682708100
3.2536-3.34930.27521460.205825182664100
3.3493-3.45740.27331390.190825662705100
3.4574-3.58090.23631480.175325562704100
3.5809-3.72430.22071380.168325602698100
3.7243-3.89370.21991530.154725532706100
3.8937-4.09880.2271240.153826042728100
4.0988-4.35540.19431390.153325432682100
4.3554-4.69140.21671360.14832597273399
4.6914-5.16290.19831270.1432598272599
5.1629-5.90870.22731310.17562609274099
5.9087-7.4390.26341480.21542621276999
7.439-45.56650.28841570.23642672282997

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