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- PDB-5ao5: Endo180 D1-4, monoclinic form -

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Basic information

Entry
Database: PDB / ID: 5ao5
TitleEndo180 D1-4, monoclinic form
ComponentsC-TYPE MANNOSE RECEPTOR 2
KeywordsENDOCYTOSIS / ENDOCYTIC RECEPTOR / FIBRONECTIN TYPE II DOMAIN / C-TYPE LECTIN DOMAIN / COLLAGEN / GELATIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / collagen catabolic process / collagen binding / endocytosis / osteoblast differentiation / signaling receptor activity / carbohydrate binding / focal adhesion / membrane
Similarity search - Function
Fibronectin, type II, collagen-binding / MRC2-like, N-terminal cysteine-rich domain / Seminal Fluid Protein PDC-109 (Domain B) / CD209-like, C-type lectin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain ...Fibronectin, type II, collagen-binding / MRC2-like, N-terminal cysteine-rich domain / Seminal Fluid Protein PDC-109 (Domain B) / CD209-like, C-type lectin-like domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C-type lectin fold / Kringle-like fold / Ribbon / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
C-type mannose receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsParacuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E.
CitationJournal: Structure / Year: 2015
Title: Insights Into Collagen Uptake by C-Type Mannose Receptors from the Crystal Structure of Endo180 Domains 1-4.
Authors: Paracuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E.
History
DepositionSep 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-TYPE MANNOSE RECEPTOR 2
B: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66110
Polymers109,1852
Non-polymers4768
Water2,936163
1
A: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8315
Polymers54,5921
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-TYPE MANNOSE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8315
Polymers54,5921
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.370, 92.370, 127.650
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C-TYPE MANNOSE RECEPTOR 2 / ENDO180 / C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER E / ENDOCYTIC RECEPTOR 180 / MACROPHAGE MANNOSE ...ENDO180 / C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER E / ENDOCYTIC RECEPTOR 180 / MACROPHAGE MANNOSE RECEPTOR 2 / UROKINASE-TYPE PLASMINOGEN ACTIVATOR RECEPTOR-ASSOCIATED PROTEIN / UPAR-ASSOCIATED PROTEIN / UROKINASE RECEPTOR-ASSOCIATED PROTEIN / CD280


Mass: 54592.484 Da / Num. of mol.: 2 / Fragment: DOMAINS 1-4, RESIDUES 35-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCEP-PU / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9UBG0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsVECTOR-DERIVED APLA AT N-TERMINUS.

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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: 3.36 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.48→62.8 Å / Num. obs: 50153 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TDQ, 3M7P, 1DQG

1tdq

3m7p

1dqg


Resolution: 2.48→60.158 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 2496 5 %
Rwork0.1936 --
obs0.1961 50150 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→60.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 24 163 7147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067221
X-RAY DIFFRACTIONf_angle_d0.9019746
X-RAY DIFFRACTIONf_dihedral_angle_d12.7332554
X-RAY DIFFRACTIONf_chiral_restr0.035983
X-RAY DIFFRACTIONf_plane_restr0.0031265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.52770.3141400.28222673X-RAY DIFFRACTION98
2.5277-2.57930.33431280.26432644X-RAY DIFFRACTION99
2.5793-2.63540.28971640.25162688X-RAY DIFFRACTION99
2.6354-2.69670.33731490.25982617X-RAY DIFFRACTION98
2.6967-2.76410.30951200.25352630X-RAY DIFFRACTION98
2.7641-2.83890.31171350.25192439X-RAY DIFFRACTION91
2.8389-2.92240.31181310.23772645X-RAY DIFFRACTION97
2.9224-3.01670.33171370.23152684X-RAY DIFFRACTION99
3.0167-3.12450.28781410.23092676X-RAY DIFFRACTION99
3.1245-3.24960.30171490.22292678X-RAY DIFFRACTION99
3.2496-3.39750.24131290.21982704X-RAY DIFFRACTION99
3.3975-3.57660.25431500.20282658X-RAY DIFFRACTION99
3.5766-3.80070.25711290.18262677X-RAY DIFFRACTION99
3.8007-4.09410.22241570.17352612X-RAY DIFFRACTION97
4.0941-4.5060.17411300.14242546X-RAY DIFFRACTION94
4.506-5.15770.18421420.14092717X-RAY DIFFRACTION99
5.1577-6.49690.19161380.17012706X-RAY DIFFRACTION99
6.4969-60.17560.24881270.18772660X-RAY DIFFRACTION95

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