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- PDB-1hup: HUMAN MANNOSE BINDING PROTEIN CARBOHYDRATE RECOGNITION DOMAIN TRI... -

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Basic information

Entry
Database: PDB / ID: 1hup
TitleHUMAN MANNOSE BINDING PROTEIN CARBOHYDRATE RECOGNITION DOMAIN TRIMERIZES THROUGH A TRIPLE ALPHA-HELICAL COILED-COIL
ComponentsMANNOSE-BINDING PROTEIN
KeywordsC-TYPE LECTIN / ALPHA-HELICAL COILED-COIL
Function / homology
Function and homology information


Lectin pathway of complement activation / positive regulation of opsonization / opsonization / complement activation, lectin pathway / negative regulation of viral process / killing by host of symbiont cells / cell surface pattern recognition receptor signaling pathway / collagen trimer / serine-type endopeptidase complex / surfactant homeostasis ...Lectin pathway of complement activation / positive regulation of opsonization / opsonization / complement activation, lectin pathway / negative regulation of viral process / killing by host of symbiont cells / cell surface pattern recognition receptor signaling pathway / collagen trimer / serine-type endopeptidase complex / surfactant homeostasis / Initial triggering of complement / D-mannose binding / complement activation, classical pathway / positive regulation of phagocytosis / antiviral innate immune response / multivesicular body / acute-phase response / calcium-dependent protein binding / response to oxidative stress / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / signaling receptor binding / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Mannose-binding protein C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSheriff, S.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Human mannose-binding protein carbohydrate recognition domain trimerizes through a triple alpha-helical coiled-coil.
Authors: Sheriff, S. / Chang, C.Y. / Ezekowitz, R.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of a Trimeric Form of Human Mannose Binding Protein
Authors: Chang, C.Y. / Sastry, K.N. / Gillies, S.D. / Ezekowitz, R.A.B. / Sheriff, S.
History
DepositionSep 21, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 14, 2015Group: Refinement description
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANNOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8896
Polymers15,6331
Non-polymers2565
Water45025
1
A: MANNOSE-BINDING PROTEIN
hetero molecules

A: MANNOSE-BINDING PROTEIN
hetero molecules

A: MANNOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66718
Polymers46,8983
Non-polymers76915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6230 Å2
ΔGint-170 kcal/mol
Surface area19690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.680, 76.680, 58.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: CIS PROLINE - PRO 193
Components on special symmetry positions
IDModelComponents
11A-304-

SO4

21A-305-

CA

31A-306-

HOH

DetailsTHE FOLLOWING TRANSFORMATIONS, WHEN APPLIED TO THE COORDINATES IN THIS ENTRY, WILL YIELD THE OTHER TWO MONOMERS OF THE TRIMER. SYMMETRY1 1 -0.499967 -0.866057 0.000000 38.33807 SYMMETRY2 1 0.865994 -0.500033 0.000000 -66.40547 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 2 -0.500033 0.866057 0.000000 76.68124 SYMMETRY2 2 -0.865994 -0.499967 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein MANNOSE-BINDING PROTEIN


Mass: 15632.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P11226
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Chang, C.Y., (1994) J.Mol.Biol., 241, 125.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
2100 mMTris-maleic acid1reservoir
318 %PEG6001reservoir
412 mg/ml1reservoirCaCl2
510 mM1reservoirNaCl

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Data collection

Diffraction sourceWavelength: 1.5418
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6978 / % possible obs: 94.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 22595 / Rmerge(I) obs: 0.088

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.1987 -
all0.1987 -
obs-6541
Displacement parametersBiso mean: 30.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 9 25 1131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 807 /
RfactorNum. reflection
Rwork0.2738 807
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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