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- PDB-1xar: Crystal Structure of a fragment of DC-SIGNR (containing the carbo... -

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Basic information

Entry
Database: PDB / ID: 1xar
TitleCrystal Structure of a fragment of DC-SIGNR (containing the carbohydrate recognition domain and two repeats of the neck).
ComponentsCD209 antigen-like protein 1
KeywordsSUGAR BINDING PROTEIN / DC-SIGNR / C-Type lectin
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / receptor-mediated endocytosis of virus by host cell / viral genome replication / peptide antigen binding / calcium-dependent protein binding / signaling receptor activity / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated virion attachment to host cell / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / extracellular region / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFeinberg, H. / Guo, Y. / Mitchell, D.A. / Drickamer, K. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Extended Neck Regions Stabilize Tetramers of the Receptors DC-SIGN and DC-SIGNR
Authors: Feinberg, H. / Guo, Y. / Mitchell, D.A. / Drickamer, K. / Weis, W.I.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD209 antigen-like protein 1
B: CD209 antigen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9016
Polymers42,8092
Non-polymers924
Water1,38777
1
A: CD209 antigen-like protein 1
B: CD209 antigen-like protein 1
hetero molecules

A: CD209 antigen-like protein 1
B: CD209 antigen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,80212
Polymers85,6184
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area6330 Å2
ΔGint-133 kcal/mol
Surface area28530 Å2
MethodPISA
2
A: CD209 antigen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4503
Polymers21,4051
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: CD209 antigen-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4503
Polymers21,4051
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.05, 82.05, 110.26
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CD209 antigen-like protein 1 / Dendritic cell-specific ICAM-3-grabbing nonintegrin 2 / DC-SIGN2 / DC-SIGN related protein / DC- ...Dendritic cell-specific ICAM-3-grabbing nonintegrin 2 / DC-SIGN2 / DC-SIGN related protein / DC-SIGNR / Liver/lymph node-specific ICAM-3-grabbing nonintegrin / L-SIGN


Mass: 21404.506 Da / Num. of mol.: 2 / Fragment: sequence database residues 216-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD209L, CD209L1 / References: UniProt: Q9H2X3
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution: 5mg/ml protein. Reservoir solution: 3.75M Sodium formate, 0.05M Tris, pH=8.5., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→59.727 Å / Num. all: 20916 / Num. obs: 20863 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 9.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.376 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→59.727 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1529759.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1020 4.9 %RANDOM
Rwork0.222 ---
obs0.222 20863 99.7 %-
all-20863 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5995 Å2 / ksol: 0.363698 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å27.19 Å20 Å2
2--6.17 Å20 Å2
3----12.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→59.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 4 77 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 150 4.4 %
Rwork0.271 3252 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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