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- PDB-3o3u: Crystal Structure of Human Receptor for Advanced Glycation Endpro... -

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Basic information

Entry
Database: PDB / ID: 3o3u
TitleCrystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)
ComponentsMaltose-binding periplasmic protein, Advanced glycosylation end product-specific receptor
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN / RAGE / AGER / scavenger receptor / macrophage cell surface receptor / innate immune receptor / Ig fold / cell surface receptor / Advanced glycation end products / AGE / Amphoterin / S100B / S100A12 / membrane / Sugar transport / Transport
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / laminin receptor activity / positive regulation of p38MAPK cascade / detection of maltose stimulus / negative regulation of interleukin-10 production / maltose transport complex / positive regulation of activated T cell proliferation / carbohydrate transport / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / carbohydrate transmembrane transporter activity / negative regulation of long-term synaptic potentiation / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of chemokine production / positive regulation of interleukin-12 production / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / outer membrane-bounded periplasmic space / postsynapse / periplasmic space / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / DNA damage response / protein-containing complex binding / cell surface / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Immunoglobulin / Immunoglobulin domain / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Immunoglobulin domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Immunoglobulin / Immunoglobulin domain / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Immunoglobulin domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltotriose / Maltose/maltodextrin-binding periplasmic protein / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsPark, H. / Boyington, J.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The 1.5 A crystal structure of human receptor for advanced glycation endproducts (RAGE) ectodomains reveals unique features determining ligand binding.
Authors: Park, H. / Boyington, J.C.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
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
N: Maltose-binding periplasmic protein, Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0353
Polymers63,4341
Non-polymers6012
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.739, 89.308, 97.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11N-615-

HOH

21N-1484-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein, Advanced glycosylation end product-specific receptor / MMBP / Maltodextrin-binding protein


Mass: 63434.012 Da / Num. of mol.: 1
Fragment: MBP: UNP residues 28-384, RAGE: UNP residues 23-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: b4034, JW3994, malE, rage, AGER / Plasmid: modified pMAL vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami pLacI (DE3) / References: UniProt: P0AEX9, UniProt: Q15109
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM Li sulfate, 100 mM Tris-HCl, pH 7.5 and 10% (w/v) polyethylene glycol 4,000 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→42 Å / Num. obs: 116451 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.057 / Net I/σ(I): 32.9
Reflection shellResolution: 1.49→1.53 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 5451 / Rsym value: 0.68 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→42.02 Å / SU ML: 0.16 / σ(F): 0.11 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 1948 1.76 %random
Rwork0.1684 ---
obs0.1686 110781 95.65 %-
all-114554 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.968 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0142 Å2-0 Å2-0 Å2
2---1.2498 Å20 Å2
3----0.7644 Å2
Refinement stepCycle: LAST / Resolution: 1.497→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 39 985 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064618
X-RAY DIFFRACTIONf_angle_d1.0476280
X-RAY DIFFRACTIONf_dihedral_angle_d14.8931702
X-RAY DIFFRACTIONf_chiral_restr0.071690
X-RAY DIFFRACTIONf_plane_restr0.005815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4972-1.55070.23441680.21099608X-RAY DIFFRACTION85
1.5507-1.61280.21431900.184710451X-RAY DIFFRACTION93
1.6128-1.68620.21641930.17410606X-RAY DIFFRACTION94
1.6862-1.77510.19121990.163810818X-RAY DIFFRACTION96
1.7751-1.88630.18761980.165210985X-RAY DIFFRACTION97
1.8863-2.03190.18931980.161811092X-RAY DIFFRACTION98
2.0319-2.23640.18391970.156911217X-RAY DIFFRACTION99
2.2364-2.55990.17192000.16511231X-RAY DIFFRACTION99
2.5599-3.22510.17912000.168411312X-RAY DIFFRACTION98
3.2251-42.03660.17082050.164911513X-RAY DIFFRACTION97
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)
10.07190.0180.0190.0180.01920.0583-0.0185-0.1412-0.10360.4770.09370.16080.09580.0149-0.00010.25190.05130.00260.11480.00580.168819.6103-1.149472.6954
20.33-0.3043-0.03290.88540.12040.3217-0.00920.0039-0.03230.06860.0310.06810.02220.0505-0.02670.08360.01970.00470.0874-0.00630.081415.702919.895964.4087
30.20070.03550.0550.22860.08060.33730.01340.0484-0.0368-0.03580.0262-0.0261-0.0120.019500.09850.01130.01610.13450.00380.103454.832425.376268.9059
40.06840.1434-0.20050.0428-0.00250.37920.00860.06320.07-0.02870.02340.0424-0.0169-0.047600.1298-0.01690.03970.17640.03980.110132.94311.9937100.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain N and resid 2:42
2X-RAY DIFFRACTION2chain N and resid 43:370
3X-RAY DIFFRACTION3chain N and resid 371:1116
4X-RAY DIFFRACTION4chain N and resid 1117:1231

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