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- PDB-5ew6: Structure of ligand binding region of uPARAP at pH 7.4 without calcium -

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Basic information

Entry
Database: PDB / ID: 5ew6
TitleStructure of ligand binding region of uPARAP at pH 7.4 without calcium
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 / osteoblast differentiation / endocytosis / 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. / Ricin-type beta-trefoil ...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 / 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 / Kringle-like fold
Similarity search - Domain/homology
triacetyl-beta-chitotriose / C-type mannose receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYuan, C. / Huang, M.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570745 China
National Natural Science Foundation of China31170707 China
National Natural Science Foundation of China31370737 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
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0156
Polymers55,8821
Non-polymers1,1335
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.110, 78.110, 252.770
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 , 1 types, 1 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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#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.: 1
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 , 3 types, 72 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 5-7% PEG 3350, 1 mM CaCl2, 100 mM HEPES, 10% PEG 3350, 5 mM EDTA

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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: Apr 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50.61 Å / Num. obs: 36396 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.079 / Rsym value: 0.085 / Net I/σ(I): 19.9
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 3 / Rsym value: 0.915 / % possible all: 100

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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: 5E4K

5e4k


Resolution: 2.29→46.192 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1749 4.82 %
Rwork0.1966 --
obs0.1986 36279 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→46.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 74 69 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083735
X-RAY DIFFRACTIONf_angle_d1.125086
X-RAY DIFFRACTIONf_dihedral_angle_d17.7152185
X-RAY DIFFRACTIONf_chiral_restr0.061525
X-RAY DIFFRACTIONf_plane_restr0.008654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.35740.31761630.28722798X-RAY DIFFRACTION100
2.3574-2.43350.29961440.24992798X-RAY DIFFRACTION100
2.4335-2.52050.2831320.23582866X-RAY DIFFRACTION100
2.5205-2.62140.28171280.21862820X-RAY DIFFRACTION100
2.6214-2.74070.27641460.22342808X-RAY DIFFRACTION100
2.7407-2.88520.25611380.21322860X-RAY DIFFRACTION100
2.8852-3.06590.27581440.21812864X-RAY DIFFRACTION100
3.0659-3.30250.24941320.2342880X-RAY DIFFRACTION100
3.3025-3.63480.24641490.20612868X-RAY DIFFRACTION100
3.6348-4.16040.24971320.18172927X-RAY DIFFRACTION100
4.1604-5.24060.17381750.15292930X-RAY DIFFRACTION100
5.2406-46.20150.23491660.18873111X-RAY DIFFRACTION99
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)
11.3245-2.20980.24846.58882.17542.3518-0.47730.3718-0.09530.9217-0.01530.02920.0843-0.2760.43340.716-0.2058-0.21710.61690.17580.5438-66.3907-101.6053509.5132
23.49862.36681.01311.90891.22091.2383-0.56880.5450.6631-0.4450.08740.0076-0.47090.271-0.0710.6833-0.4356-0.36150.83480.35230.7856-55.7723-94.6987496.5627
36.42365.7083-5.85457.2914-6.54497.56270.1385-0.00631.0622-0.29690.08330.327-0.3745-0.2569-0.3890.8395-0.3544-0.32890.63990.22790.9438-57.5337-89.7988502.7971
44.86192.29390.32014.8001-0.93240.3386-0.2660.53340.3916-0.5880.25670.110.4386-0.39390.06770.8865-0.3974-0.30470.69790.26450.6076-65.6676-102.8655498.9954
58.8228-3.2229-3.8195.36524.10323.4045-0.3579-0.1968-0.7371-0.8809-0.8060.3761-1.5766-0.2341.53531.7228-0.3489-0.19751.3203-0.13130.6804-58.4191-108.0357482.1729
63.7157-0.99860.32053.168-1.3681.1715-0.53921.1567-0.3316-1.30540.4079-0.25480.81710.1163-0.10381.2923-0.4152-0.04860.9370.10720.6241-59.3172-106.2854491.3721
74.6253.3217-1.75454.8014-0.82414.2726-0.2937-0.1292-0.4369-0.38740.1849-0.82080.17670.54650.07420.6233-0.1675-0.28620.46290.18870.6659-53.1777-103.6982505.1675
81.58770.9769-0.21921.21380.30880.3411-0.28740.64490.555-0.47270.31140.7032-0.0874-0.27030.37420.7197-0.7316-0.44640.85520.50490.9579-77.5976-112.5583503.7653
91.73160.95391.78883.6137-0.55044.23190.0082-0.02120.25240.12190.36170.532-0.1926-0.60310.66850.755-0.3909-0.36070.90230.470.9497-83.5149-110.2095504.1537
101.87630.4117-0.7632.4039-0.78980.472-0.2154-0.25220.38640.49220.0707-0.028-0.40960.2851-0.47550.6976-0.2711-0.34610.49110.09650.7516-82.1857-114.5578521.66
110.40330.60540.80624.7704-0.5312.4264-0.21210.14560.4516-0.04920.04520.2198-0.38550.35890.10890.5635-0.2507-0.24310.61490.17150.6402-75.9243-123.7943522.0035
121.3825-1.8944-1.00654.55491.99464.0081-0.1658-0.0104-0.1355-0.04930.3821-0.47070.69580.0889-0.14570.6435-0.1748-0.22330.45680.16350.5752-75.1859-131.1671525.3592
136.2957-0.4226-0.48314.4073-0.00273.6688-0.21450.5291-0.2806-0.4795-0.05080.07210.8401-0.5489-0.25970.8195-0.2143-0.33170.5280.1190.4209-70.8673-138.7171527.6291
142.63261.06280.00410.7540.59931.1008-0.020.2573-0.67810.05740.1838-0.19560.8164-0.0658-0.56790.7649-0.3233-0.30760.52260.11120.5915-76.0606-133.9052520.2989
150.46980.3253-0.18040.73890.24680.3406-0.9232-0.04710.96581.4902-0.1367-1.0728-0.87020.06671.21271.0882-0.0298-0.54550.7486-0.05851.0714-55.1107-122.961551.8961
165.99222.6990.90953.9257-1.29723.5264-0.33330.038-0.05690.15760.3061-0.64610.67550.47620.05480.7650.1885-0.28850.466-0.11860.5954-56.2852-142.4727552.9762
171.08030.105-0.1712.949-1.69049.8123-0.4932-0.16180.46220.3079-0.0146-0.5729-0.43110.85490.11450.57230.0907-0.30070.4754-0.04070.6436-57.6391-131.9364549.4596
183.93631.1117-0.27453.6731-1.53828.2806-0.10470.212-0.01490.29990.216-0.43420.57270.51650.04530.660.1591-0.25720.4466-0.05430.5483-60.0071-137.8982543.8125
190.7514-0.439-1.17113.13950.16242.1345-0.12620.34680.6865-0.01250.05990.214-0.15860.0836-0.09710.50840.0628-0.26880.53910.02020.5697-64.168-131.5328540.8834
204.3760.2541-1.36212.5574-1.64694.256-0.18320.5547-0.1109-0.22970.3636-0.48840.60660.3575-0.10510.78350.141-0.31670.4824-0.07180.6038-60.2535-139.239542.3887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 37:45)
2X-RAY DIFFRACTION2(chain A and resid 46:64)
3X-RAY DIFFRACTION3(chain A and resid 65:70)
4X-RAY DIFFRACTION4(chain A and resid 71:95)
5X-RAY DIFFRACTION5(chain A and resid 96:106)
6X-RAY DIFFRACTION6(chain A and resid 107:137)
7X-RAY DIFFRACTION7(chain A and resid 138:172)
8X-RAY DIFFRACTION8(chain A and resid 173:200)
9X-RAY DIFFRACTION9(chain A and resid 201:223)
10X-RAY DIFFRACTION10(chain A and resid 224:245)
11X-RAY DIFFRACTION11(chain A and resid 246:280)
12X-RAY DIFFRACTION12(chain A and resid 281:313)
13X-RAY DIFFRACTION13(chain A and resid 314:332)
14X-RAY DIFFRACTION14(chain A and resid 333:361)
15X-RAY DIFFRACTION15(chain A and resid 362:394)
16X-RAY DIFFRACTION16(chain A and resid 395:405)
17X-RAY DIFFRACTION17(chain A and resid 406:430)
18X-RAY DIFFRACTION18(chain A and resid 431:453)
19X-RAY DIFFRACTION19(chain A and resid 454:468)
20X-RAY DIFFRACTION20(chain A and resid 469:511)

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