[English] 日本語
Yorodumi
- PDB-5e4l: Structure of ligand binding region of uPARAP at pH 5.3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e4l
TitleStructure of ligand binding region of uPARAP at pH 5.3
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
C-type mannose receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsYuan, C. / Huang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Natural Science Foundation Of China31570745 China
CitationJournal: to be published
Title: Crystal structures of uPARAP, a member of mannose receptor family
Authors: Yuan, C. / Huang, M.
History
DepositionOct 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,44710
Polymers111,7642
Non-polymers6838
Water3,639202
1
A: C-type mannose receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2235
Polymers55,8821
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-10 kcal/mol
Surface area21650 Å2
MethodPISA
2
B: C-type mannose receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2235
Polymers55,8821
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint2 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.270, 102.700, 87.760
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 55881.840 Da / Num. of mol.: 2 / 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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 8-12% (w/v) PEG 3350, 200 mM NaCl, 35 mM CaCl2, 50 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.44→54.43 Å / Num. obs: 48904 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.2
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

-
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: 1QO6, 1TDQ

1qo6

1tdq


Resolution: 2.44→54.43 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 2441 4.99 %
Rwork0.2173 --
obs0.2194 48899 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→54.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 34 202 6747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086741
X-RAY DIFFRACTIONf_angle_d1.029176
X-RAY DIFFRACTIONf_dihedral_angle_d13.7593943
X-RAY DIFFRACTIONf_chiral_restr0.059938
X-RAY DIFFRACTIONf_plane_restr0.0071191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.48980.31061480.2732720X-RAY DIFFRACTION100
2.4898-2.5440.29741450.25022720X-RAY DIFFRACTION100
2.544-2.60310.30481360.25322702X-RAY DIFFRACTION100
2.6031-2.66820.25771620.25562716X-RAY DIFFRACTION100
2.6682-2.74040.35271390.23992732X-RAY DIFFRACTION100
2.7404-2.8210.28241280.24172733X-RAY DIFFRACTION100
2.821-2.9120.29371520.252716X-RAY DIFFRACTION100
2.912-3.01610.31631400.24582729X-RAY DIFFRACTION100
3.0161-3.13690.31581220.23762750X-RAY DIFFRACTION100
3.1369-3.27960.29031420.23572706X-RAY DIFFRACTION100
3.2796-3.45250.27831380.24492731X-RAY DIFFRACTION100
3.4525-3.66880.26031140.23052775X-RAY DIFFRACTION100
3.6688-3.9520.27021270.20662774X-RAY DIFFRACTION100
3.952-4.34950.27891480.18822711X-RAY DIFFRACTION100
4.3495-4.97850.18681680.1712728X-RAY DIFFRACTION100
4.9785-6.27090.20241700.19032738X-RAY DIFFRACTION100
6.2709-54.4440.24951620.21512777X-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)
11.4922.2729-0.54073.6498-1.2382-0.3050.15980.01690.16760.3863-0.09130.1332-0.0297-0.0790.00020.3709-0.05570.03770.373-0.01190.3551217.3549-8.613890.5857
21.0047-0.2368-0.45012.3522-0.97232.4112-0.0732-0.2416-0.07461.4772-0.0007-0.2108-0.3080.53850.55690.9167-0.0294-0.14740.39690.02880.1509212.1871-41.1912121.6316
31.26632.52360.52383.01141.7408-0.59220.29320.0159-0.39720.58-0.1424-0.53460.08430.10520.0280.377-0.0875-0.10190.41090.03840.6034176.6507-86.599890.7086
41.26130.77840.11191.925-0.02331.54040.6967-0.6269-0.08271.363-0.64650.20290.1453-0.65590.51890.6243-0.28930.17410.6823-0.04340.3508185.6436-55.143112.3337
50.2667-0.15330.14330.30470.33960.4837-0.1381-0.23770.3519-0.03460.10920.5921-0.3589-0.873-0.96851.8521-0.31250.79891.6137-0.1760.8189176.3148-47.9601132.6161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 227 )
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 506 )
3X-RAY DIFFRACTION3chain 'B' and (resid 40 through 227 )
4X-RAY DIFFRACTION4chain 'B' and (resid 228 through 462 )
5X-RAY DIFFRACTION5chain 'B' and (resid 463 through 505 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more