[English] 日本語
Yorodumi
- PDB-1r1z: The Crystal structure of the Carbohydrate recognition domain of t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r1z
TitleThe Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding
ComponentsERGIC-53 proteinVesicular-tubular cluster
KeywordsSUGAR BINDING PROTEIN / beta-sheet / calcium-binding / lectin / mammalian / endoplasmic reticulum
Function / homology
Function and homology information


RHOD GTPase cycle / : / RHOG GTPase cycle / RAC2 GTPase cycle / : / RHOA GTPase cycle / positive regulation of organelle organization / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum organization ...RHOD GTPase cycle / : / RHOG GTPase cycle / RAC2 GTPase cycle / : / RHOA GTPase cycle / positive regulation of organelle organization / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum organization / COPII-coated ER to Golgi transport vesicle / Golgi organization / mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / protein transport / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / identical protein binding / metal ion binding
Similarity search - Function
Legume-like lectin / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVelloso, L.M. / Svensson, K. / Pettersson, R.F. / Lindqvist, Y.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated ...Title: The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated with Calcium Ion Binding.
Authors: Velloso, L.M. / Svensson, K. / Pettersson, R.F. / Lindqvist, Y.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERGIC-53 protein
B: ERGIC-53 protein
C: ERGIC-53 protein
D: ERGIC-53 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,43012
Polymers116,1094
Non-polymers3218
Water3,477193
1
A: ERGIC-53 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1073
Polymers29,0271
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERGIC-53 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1073
Polymers29,0271
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ERGIC-53 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1073
Polymers29,0271
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ERGIC-53 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1073
Polymers29,0271
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.351, 81.068, 82.306
Angle α, β, γ (deg.)91.05, 94.14, 94.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHEAA54 - 27333 - 252
21PHEPHEPHEPHEBB54 - 27333 - 252
31PHEPHEPHEPHECC54 - 27333 - 252
41PHEPHEPHEPHEDD54 - 27333 - 252
52HISHISGLYGLYAA28 - 447 - 23
62HISHISALAALABB25 - 447 - 26
72HISHISALAALACC25 - 447 - 26
82HISHISALAALADD25 - 447 - 26

-
Components

#1: Protein
ERGIC-53 protein / Vesicular-tubular cluster / ER-Golgi intermediate compartment 53 kDa protein / Lectin / mannose-binding 1 / p58


Mass: 29027.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: LMAN1 OR ERGIC53 / Plasmid: pFastbac / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62902
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Calcium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris1droppH7.5
325 %(w/v)PEG80001reservoir
42 mM1reservoirCaCl2
5100 mMsodium HEPES1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. all: 98470 / Num. obs: 42617 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.096 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6205 / Rsym value: 0.33 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 42111 / % possible obs: 94.6 % / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gv9

1gv9


Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.516 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0.005 / σ(I): 0.005 / ESU R: 0.49 / ESU R Free: 0.259 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24063 1071 2.5 %RANDOM
Rwork0.2225 ---
all0.223 42617 --
obs0.22297 41040 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.012 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-2.51 Å2-1.35 Å2
2---3.33 Å20.89 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 8 193 7793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217812
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.89910616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565980
X-RAY DIFFRACTIONr_chiral_restr0.0890.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026216
X-RAY DIFFRACTIONr_nbd_refined0.2230.22849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2338
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4250.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.28
X-RAY DIFFRACTIONr_mcbond_it0.4961.54876
X-RAY DIFFRACTIONr_mcangle_it0.94427776
X-RAY DIFFRACTIONr_scbond_it1.45732936
X-RAY DIFFRACTIONr_scangle_it2.334.52840
Refine LS restraints NCS

Ens-ID: 1 / Number: 1833 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.040.05
4Dtight positional0.040.05
1Atight thermal0.130.5
2Btight thermal0.110.5
3Ctight thermal0.080.5
4Dtight thermal0.090.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 90 -
Rwork0.273 3082 -
obs-6205 95.7 %
Refinement
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.24

+
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://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