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- PDB-4gkx: Crystal structure of a carbohydrate-binding domain -

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Basic information

Entry
Database: PDB / ID: 4gkx
TitleCrystal structure of a carbohydrate-binding domain
ComponentsProtein ERGIC-53
KeywordsPROTEIN TRANSPORT / Endoplasmic reticulum
Function / homology
Function and homology information


Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / mannose binding / RHOG GTPase cycle / RHOA GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / RAC3 GTPase cycle / RAC2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / unfolded protein binding / blood coagulation / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular exosome / membrane / 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
2alpha-alpha-mannobiose / Protein ERGIC-53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPage, R.C. / Zheng, C. / Nix, J.C. / Misra, S. / Zhang, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Characterization of Carbohydrate Binding by LMAN1 Protein Provides New Insight into the Endoplasmic Reticulum Export of Factors V (FV) and VIII (FVIII).
Authors: Zheng, C. / Page, R.C. / Das, V. / Nix, J.C. / Wigren, E. / Misra, S. / Zhang, B.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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: Protein ERGIC-53
B: Protein ERGIC-53
C: Protein ERGIC-53
D: Protein ERGIC-53
E: Protein ERGIC-53
F: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,21631
Polymers172,0376
Non-polymers3,17925
Water5,999333
1
A: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5569
Polymers28,6731
Non-polymers8838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1875
Polymers28,6731
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1875
Polymers28,6731
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0954
Polymers28,6731
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0954
Polymers28,6731
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0954
Polymers28,6731
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.283, 111.498, 111.388
Angle α, β, γ (deg.)60.09, 89.21, 86.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 41:269 ) and (not element H)
211chain 'B' and (resseq 41:269 ) and (not element H)
311chain 'C' and (resseq 41:269 ) and (not element H)
411chain 'D' and (resseq 41:269 ) and (not element H)
511chain 'E' and (resseq 41:269 ) and (not element H)
611chain 'F' and (resseq 41:269 ) and (not element H)

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Components

#1: Protein
Protein ERGIC-53 / ER-Golgi intermediate compartment 53 kDa protein / Gp58 / Intracellular mannose-specific lectin ...ER-Golgi intermediate compartment 53 kDa protein / Gp58 / Intracellular mannose-specific lectin MR60 / Lectin mannose-binding 1


Mass: 28672.803 Da / Num. of mol.: 6
Fragment: Carbohydrate Recognition Domain (UNP Residues 31-270)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERGIC53, F5F8D, LMAN1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P49257
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 17% PEG 8000, 0.002M calcium chloride, 0.01M alpha-1,2-dimannose, 0.05M sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 25, 2012
RadiationMonochromator: sagitally focused double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→39.19 Å / Num. all: 43492 / Num. obs: 43492 / % possible obs: 96.9 % / Observed criterion σ(F): 6.4 / Observed criterion σ(I): 6.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A4U

3a4u


Resolution: 2.7→37.191 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 2166 4.99 %RANDOM
Rwork0.2458 ---
obs0.2478 43446 96.76 %-
all-43447 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→37.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10842 0 192 333 11367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211343
X-RAY DIFFRACTIONf_angle_d1.33915409
X-RAY DIFFRACTIONf_dihedral_angle_d14.8553974
X-RAY DIFFRACTIONf_chiral_restr0.0881621
X-RAY DIFFRACTIONf_plane_restr0.0082030
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1799X-RAY DIFFRACTIONPOSITIONAL0.66
12B1799X-RAY DIFFRACTIONPOSITIONAL0.66
13C1799X-RAY DIFFRACTIONPOSITIONAL0.678
14D1790X-RAY DIFFRACTIONPOSITIONAL0.634
15E1799X-RAY DIFFRACTIONPOSITIONAL0.643
16F1799X-RAY DIFFRACTIONPOSITIONAL0.636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76280.38571500.34222794X-RAY DIFFRACTION98
2.7628-2.83190.3841560.33022780X-RAY DIFFRACTION98
2.8319-2.90840.47911470.34082713X-RAY DIFFRACTION98
2.9084-2.9940.41831500.34182854X-RAY DIFFRACTION98
2.994-3.09060.38161450.31752760X-RAY DIFFRACTION98
3.0906-3.2010.39681730.322752X-RAY DIFFRACTION98
3.201-3.32910.371400.2932794X-RAY DIFFRACTION98
3.3291-3.48050.33551500.28692758X-RAY DIFFRACTION98
3.4805-3.66380.26161350.26732753X-RAY DIFFRACTION97
3.6638-3.89310.29361500.25752783X-RAY DIFFRACTION97
3.8931-4.19340.28021250.23262715X-RAY DIFFRACTION96
4.1934-4.61470.21831290.19722714X-RAY DIFFRACTION94
4.6147-5.28080.24761520.19392697X-RAY DIFFRACTION95
5.2808-6.6470.26021370.23032758X-RAY DIFFRACTION96
6.647-37.19490.21011270.2012655X-RAY DIFFRACTION93

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