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- PDB-3cjj: Crystal structure of human rage ligand-binding domain -

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Basic information

Entry
Database: PDB / ID: 3cjj
TitleCrystal structure of human rage ligand-binding domain
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsMEMBRANE PROTEIN / SIGNALING PROTEIN / immunoglobulin domain / Glycoprotein / Membrane / Secreted / Transmembrane
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / positive regulation of DNA-templated DNA replication / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression ...regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / positive regulation of DNA-templated DNA replication / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / transcytosis / induction of positive chemotaxis / S100 protein binding / positive regulation of monocyte chemotactic protein-1 production / regulation of long-term synaptic potentiation / positive regulation of p38MAPK cascade / positive regulation of heterotypic cell-cell adhesion / negative regulation of connective tissue replacement involved in inflammatory response wound healing / positive regulation of activated T cell proliferation / protein localization to membrane / scavenger receptor activity / regulation of spontaneous synaptic transmission / negative regulation of interleukin-10 production / positive regulation of double-strand break repair / laminin receptor activity / response to amyloid-beta / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / phagocytosis / transport across blood-brain barrier / phagocytic cup / positive regulation of chemokine production / positive regulation of interleukin-12 production / astrocyte activation / : / positive regulation of interleukin-1 beta production / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / response to wounding / regulation of synaptic plasticity / positive regulation of interleukin-6 production / positive regulation of JNK cascade / cellular response to amyloid-beta / fibrillar center / neuron projection development / positive regulation of tumor necrosis factor production / cell junction / transmembrane signaling receptor activity / amyloid-beta binding / signaling receptor activity / regulation of inflammatory response / histone binding / molecular adaptor activity / learning or memory / response to hypoxia / early endosome / positive regulation of ERK1 and ERK2 cascade / DNA replication / cell surface receptor signaling pathway / apical plasma membrane / postsynapse / inflammatory response / DNA repair / protein-containing complex binding / cell surface / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsKoch, M. / Dattilo, B.M. / Schiefner, A. / Diez, J. / Chazin, W.J. / Fritz, G.
CitationJournal: Structure / Year: 2010
Title: Structural basis for ligand recognition and activation of RAGE.
Authors: Koch, M. / Chitayat, S. / Dattilo, B.M. / Schiefner, A. / Diez, J. / Chazin, W.J. / Fritz, G.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
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_ref_seq_dif / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _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: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3296
Polymers24,0091
Non-polymers3215
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.850, 119.960, 28.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 24008.531 Da / Num. of mol.: 1 / Fragment: V and C1 domain, ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Origami B / References: UniProt: Q15109
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na cacodylate, 0.2M Zn acetate, 11% PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008, 1.28, 1.283
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2006
RadiationMonochromator: Al FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.281
31.2831
ReflectionAv σ(I) over netI: 10.5 / Number: 127070 / Rmerge(I) obs: 0.073 / D res high: 2 Å / Num. obs: 33893 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1035.182097810.032
61098599.210.04
5691210010.045
45206699.910.052
34582099.810.065
2.73374299.910.084
2.22.71168810010.145
22.2847110010.276
ReflectionResolution: 1.85→35.18 Å / Num. obs: 23066 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.657 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-20.5893.23354147121100
2-2.20.29963191944841100
2.2-2.70.15710.54407262401100
2.7-30.09316.71396620231100
3-40.072212143531871100
4-50.05623.1776611631100
5-60.04822.834385241100
6-100.04622.43719590199.2
10-35.180.04119.9710143177.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.375 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1154 5 %RANDOM
Rwork0.209 ---
obs0.21 23063 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.05 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 8 229 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221752
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9822389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1275224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08223.23971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1051516
X-RAY DIFFRACTIONr_chiral_restr0.1180.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021347
X-RAY DIFFRACTIONr_nbd_refined0.2390.2770
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2180
X-RAY DIFFRACTIONr_metal_ion_refined0.2020.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.226
X-RAY DIFFRACTIONr_mcbond_it1.1461.51139
X-RAY DIFFRACTIONr_mcangle_it1.87621804
X-RAY DIFFRACTIONr_scbond_it2.6953694
X-RAY DIFFRACTIONr_scangle_it4.4664.5582
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 84 -
Rwork0.275 1595 -
all-1679 -
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)
12.9504-0.2360.29784.0614-1.19470.92670.1025-0.1309-0.4383-0.031-0.1556-0.32210.04460.01870.05310.1136-0.0058-0.01740.06710.02760.044848.0472.82512.239
22.3318-1.96351.81112.9834-2.3892.51-0.03430.16950.33650.1198-0.1555-0.1816-0.13910.10830.18980.09780.0317-0.01320.05750.0517-0.00334.69538.963-5.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 1231 - 102
2X-RAY DIFFRACTION2AA124 - 240103 - 219

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