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- PDB-5e4k: Structure of ligand binding region of uPARAP at pH 7.4 -

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Basic information

Entry
Database: PDB / ID: 5e4k
TitleStructure of ligand binding region of uPARAP at pH 7.4
ComponentsC-type mannose receptor 2
KeywordsSUGAR BINDING PROTEIN / endocytic collagen receptor
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
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. ...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 / C-type lectin fold / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Kringle-like fold / 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: 2.58 Å
AuthorsYuan, C. / Huang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570745 China
CitationJournal: Biochem.J. / Year: 2016
Title: Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding
Authors: Yuan, C. / Jurgensen, H.J. / Engelholm, L.H. / Li, R. / Liu, M. / Jiang, L. / Luo, Z. / Behrendt, N. / Huang, M.
History
DepositionOct 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type mannose receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0648
Polymers55,8821
Non-polymers1,1827
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-8 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.940, 74.940, 224.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein C-type mannose receptor 2 / uPARAP


Mass: 55881.840 Da / Num. of mol.: 1 / Fragment: ligand binding region, UNP residues 31-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRC2, CLEC13E, ENDO180, KIAA0709, UPARAP / Plasmid: PMT/BIP / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 Cells / References: UniProt: Q9UBG0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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 , 5 types, 31 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 5-7% PEG 3350, 1 mM CaCl2, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.58→37.47 Å / Num. obs: 20523 / % possible obs: 98.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.102 / Net I/σ(I): 13
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.812 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data scaling
PDB_EXTRACT3.15data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4L

5e4l


Resolution: 2.58→37.47 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1017 4.96 %
Rwork0.2144 --
obs0.2165 20523 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 74 26 3435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093514
X-RAY DIFFRACTIONf_angle_d1.5474783
X-RAY DIFFRACTIONf_dihedral_angle_d12.6572757
X-RAY DIFFRACTIONf_chiral_restr0.071495
X-RAY DIFFRACTIONf_plane_restr0.01613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5801-2.71610.39761380.31632739X-RAY DIFFRACTION99
2.7161-2.88620.35281580.28062761X-RAY DIFFRACTION99
2.8862-3.10890.32111480.27612746X-RAY DIFFRACTION98
3.1089-3.42160.29991230.2392785X-RAY DIFFRACTION98
3.4216-3.91630.30531580.21642741X-RAY DIFFRACTION97
3.9163-4.93230.19861360.1792806X-RAY DIFFRACTION97
4.9323-37.47390.21621560.19682928X-RAY DIFFRACTION95
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)
11.97790.0625-1.89490.1675-0.45892.7637-0.05270.50620.0076-0.23630.3107-0.2651-0.3488-0.0503-1.33720.4552-0.24920.20410.7767-0.33170.5495-9.745328.7875-0.4829
21.67771.3610.59871.99730.21650.4195-0.0165-0.09770.1704-0.0093-0.03780.2985-0.0304-0.03020.06290.9363-0.63240.1281.3196-0.41641.1995-16.497723.192911.87
30.79490.31750.06030.2504-0.12130.37140.1543-0.09160.07150.201-0.07710.2007-0.08270.01570.25450.7158-0.52970.34371.1136-0.39270.8103-10.86930.84098.325
42.21641.07992.87494.15733.43376.15230.225-0.37830.0110.2621-0.16240.10080.6471-0.41330.07521.3336-0.68230.30031.6418-0.60210.9673-8.23734.972617.799
50.6305-1.2286-0.53897.1636.02876.12280.00780.03360.13170.08730.5901-0.6786-0.40370.9277-0.6211.3285-0.7420.00881.5262-0.13360.5843-0.630529.041515.7681
60.2443-0.6181-0.64062.11942.30792.52961.055-0.8805-0.72452.1793-0.4835-0.34041.7972-0.7955-0.67151.4598-0.7422-0.01511.353-0.20460.7352-5.735119.195116.6566
70.96030.50810.69010.95630.45270.50850.05110.0382-0.0753-0.0267-0.02110.06260.05590.0313-0.70590.8429-0.5510.11361.2094-0.47630.8833-5.898520.72474.8585
80.04930.1212-0.40220.2973-1.00753.40520.3102-0.24750.69850.4956-0.17440.3351-0.8141-0.3458-0.42950.9443-0.36450.44681.0332-0.51171.10390.121645.00420.8423
92.8653-0.42860.98983.91672.41469.96210.6596-0.24380.8050.7191-0.0592-0.0791-1.3812-0.21240.26131.0407-0.2640.51351.1523-0.53531.32690.136850.05910.792
109.5921-1.3815-1.60254.6061-2.59744.7966-0.55132.0277-0.248-0.81-0.05140.8635-0.10030.20660.38910.6279-0.33430.14810.827-0.17980.74070.686843.2089-12.1552
117.6271-3.7483-5.95429.42896.40836.2470.90591.16030.2664-0.8106-1.10781.024-1.5447-1.27340.13090.55440.00410.11960.6851-0.16720.69767.889344.9235-22.7799
122.4694-0.2802-0.05273.01763.61764.37330.3785-0.34370.53070.3765-0.28260.6523-0.0019-0.20730.01740.6222-0.30080.1650.7129-0.2640.660113.549537.5017-14.331
133.64231.41621.6353.81133.15414.03590.5206-0.0561-0.43760.2754-0.0442-0.3866-0.17080.569-0.40550.5139-0.16720.18780.5785-0.25250.683222.493836.1748-19.8842
141.12661.15021.24662.46871.66854.37320.3634-0.0037-0.050.34020.2712-0.63490.56650.63960.00390.6147-0.18430.11110.7481-0.45210.679727.570437.1413-13.5923
150.1101-0.02-0.06660.00430.0150.03880.07430.1247-0.0183-0.1360.00810.22320.14660.03870.7770.4362-0.2293-0.11090.5136-0.26290.502413.14632.7947-21.101
160.1140.07760.21380.24660.23230.44040.05260.1517-0.1118-0.05110.11970.02220.21020.0904-0.17881.5092-0.5941-0.03051.1874-0.59031.571616.72297.0866-43.5222
170.4342-0.2727-0.86170.1710.54081.7084-0.33190.675-0.87480.2678-0.31470.69830.5729-0.5743-0.13480.45270.10350.02760.7242-0.42740.989628.142512.394-42.7638
182.0783-1.1065-0.91162.29782.74025.6301-0.22970.2582-0.52310.5242-0.47810.80311.0405-0.47010.52160.601-0.0290.13390.8699-0.37250.729324.594819.3524-36.3226
192.4039-0.7537-2.59296.415-4.23068.6223-0.3349-1.36280.40881.1644-0.0339-1.3350.23241.06580.21060.7963-0.0174-0.03581.2062-0.27150.717733.829623.5538-28.0231
201.37380.78110.89633.29352.09554.0352-0.2561-0.18240.04490.83580.1546-0.01380.62680.2813-1.38220.57090.08840.00860.6308-0.3920.617230.437217.4364-35.0616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 37:47)
2X-RAY DIFFRACTION2(chain A and resid 48:62)
3X-RAY DIFFRACTION3(chain A and resid 63:96)
4X-RAY DIFFRACTION4(chain A and resid 105:113)
5X-RAY DIFFRACTION5(chain A and resid 114:125)
6X-RAY DIFFRACTION6(chain A and resid 126:132)
7X-RAY DIFFRACTION7(chain A and resid 133:173)
8X-RAY DIFFRACTION8(chain A and resid 174:205)
9X-RAY DIFFRACTION9(chain A and resid 206:224)
10X-RAY DIFFRACTION10(chain A and resid 225:235)
11X-RAY DIFFRACTION11(chain A and resid 236:252)
12X-RAY DIFFRACTION12(chain A and resid 253:280)
13X-RAY DIFFRACTION13(chain A and resid 281:328)
14X-RAY DIFFRACTION14(chain A and resid 329:351)
15X-RAY DIFFRACTION15(chain A and resid 352:382)
16X-RAY DIFFRACTION16(chain A and resid 383:391)
17X-RAY DIFFRACTION17(chain A and resid 392:403)
18X-RAY DIFFRACTION18(chain A and resid 404:467)
19X-RAY DIFFRACTION19(chain A and resid 468:487)
20X-RAY DIFFRACTION20(chain A and resid 488:506)

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