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- PDB-1r1z: The Crystal structure of the Carbohydrate recognition domain of t... -

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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 protein
KeywordsSUGAR BINDING PROTEIN / beta-sheet / calcium-binding / lectin / mammalian / endoplasmic reticulum
Function / homology
Function and homology information


RHOD GTPase cycle / postsynaptic Golgi apparatus / RAC2 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / positive regulation of organelle organization / Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization ...RHOD GTPase cycle / postsynaptic Golgi apparatus / RAC2 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / positive regulation of organelle organization / Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum organization / endoplasmic reticulum-Golgi intermediate compartment / Golgi organization / D-mannose binding / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / protein transport / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / metal ion binding / identical protein 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein
ERGIC-53 protein / 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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 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

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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

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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

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