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- PDB-5gqq: Structure of ALG-2/HEBP2 Complex -

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Basic information

Entry
Database: PDB / ID: 5gqq
TitleStructure of ALG-2/HEBP2 Complex
Components
  • Heme-binding protein 2
  • Programmed cell death protein 6
KeywordsAPOPTOSIS / EF Hands / complex / Calcium ions
Function / homology
Function and homology information


neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin-like ligase-substrate adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / apoptotic signaling pathway / intracellular protein transport / response to calcium ion / calcium-dependent protein binding / positive regulation of angiogenesis / azurophil granule lumen / protein-macromolecule adaptor activity / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / calcium ion binding / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SOUL haem-binding protein / SOUL heme-binding protein / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...SOUL haem-binding protein / SOUL heme-binding protein / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Programmed cell death protein 6 / Heme-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, X. / Ma, J. / Zhang, H. / Feng, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370925 China
National Key Project on Major Infectious Diseases from the Ministry of Science and Technology2012ZX10001-008 China
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural and Functional Study of Apoptosis-linked Gene-2Heme-binding Protein 2 Interactions in HIV-1 Production.
Authors: Ma, J. / Zhang, X. / Feng, Y. / Zhang, H. / Wang, X. / Zheng, Y. / Qiao, W. / Liu, X.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Derived calculations
Category: citation / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme-binding protein 2
B: Heme-binding protein 2
C: Programmed cell death protein 6
D: Programmed cell death protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,44712
Polymers80,1354
Non-polymers3118
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-150 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.279, 78.124, 87.171
Angle α, β, γ (deg.)113.71, 105.64, 93.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Heme-binding protein 2 / Placental protein 23 / PP23 / Protein SOUL


Mass: 20117.422 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEBP2, C6orf34, SOUL
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9Y5Z4
#2: Protein Programmed cell death protein 6 / / Apoptosis-linked gene 2 protein / Probable calcium-binding protein ALG-2


Mass: 19950.195 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6, ALG2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: O75340
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris, 2 M NaCl, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / % possible obs: 94.94 % / Redundancy: 1.9 % / Net I/σ(I): 18.78

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Processing

Software
NameVersionClassification
HKL-2000data scaling
AUTOMARmodel building
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.935 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 25.11
RfactorNum. reflection% reflection
Rfree0.2251 2632 5.07 %
Rwork0.1942 --
obs0.1958 51901 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→25.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5633 0 8 307 5948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085771
X-RAY DIFFRACTIONf_angle_d1.2087815
X-RAY DIFFRACTIONf_dihedral_angle_d16.8212125
X-RAY DIFFRACTIONf_chiral_restr0.082819
X-RAY DIFFRACTIONf_plane_restr0.0061023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.24020.32481340.28842544X-RAY DIFFRACTION91
2.2402-2.28330.29261400.26792575X-RAY DIFFRACTION97
2.2833-2.32990.31591420.26582642X-RAY DIFFRACTION97
2.3299-2.38050.29291450.24732697X-RAY DIFFRACTION97
2.3805-2.43580.2981500.26162619X-RAY DIFFRACTION97
2.4358-2.49670.26611430.2462680X-RAY DIFFRACTION97
2.4967-2.56410.32971200.23422645X-RAY DIFFRACTION97
2.5641-2.63950.26771270.21962674X-RAY DIFFRACTION97
2.6395-2.72460.2071140.21832666X-RAY DIFFRACTION97
2.7246-2.82190.27021490.21422633X-RAY DIFFRACTION97
2.8219-2.93470.26241370.21142634X-RAY DIFFRACTION96
2.9347-3.06810.21991400.21172599X-RAY DIFFRACTION96
3.0681-3.22960.24211610.19952612X-RAY DIFFRACTION95
3.2296-3.43150.22871400.22553X-RAY DIFFRACTION94
3.4315-3.69580.23941410.19142570X-RAY DIFFRACTION94
3.6958-4.06640.2151360.17312523X-RAY DIFFRACTION93
4.0664-4.65190.17971340.15092493X-RAY DIFFRACTION91
4.6519-5.84980.17931480.15982558X-RAY DIFFRACTION94
5.8498-25.93670.18511310.17322352X-RAY DIFFRACTION87

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