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- PDB-1iiy: Solution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,... -

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Basic information

Entry
Database: PDB / ID: 1iiy
TitleSolution NMR Structure of Complex of 1:2 Cyanovirin-N:Man-Alpha1,2-Man-Alpha Restrained Regularized Mean Coordinates
ComponentsCYANOVIRIN-N
KeywordsANTIVIRAL PROTEIN / HIV-INACTIVATING PROTEIN / MAN-ALPHA1 / 2-MAN-ALPHA
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
2alpha-alpha-mannobiose / Cyanovirin-N
Similarity search - Component
Biological speciesNostoc ellipsosporum (bacteria)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsBewley, C.A.
CitationJournal: Structure / Year: 2001
Title: Solution Structure of a Cyanovirin-N:Man alpha 1-2Man alpha Complex. Structural Basis for High Affinity Carbohydrate-Mediated Binding to gp120
Authors: Bewley, C.A.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYANOVIRIN-N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7073
Polymers11,0221
Non-polymers6852
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50
Representative

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Components

#1: Protein CYANOVIRIN-N


Mass: 11022.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc ellipsosporum (bacteria) / References: UniProt: P81180
#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.: 2
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
Has protein modificationY
Nonpolymer detailsRESIDUE NUMBERING: CVN:1-101 MAN:201/202 (CHAIN B) CORRESPONDS TO MAN-ALPHA-1,2-MAN-ALPHA BOUND ...RESIDUE NUMBERING: CVN:1-101 MAN:201/202 (CHAIN B) CORRESPONDS TO MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE HIGH AFFINITY SITE WITH C1-C6 of MAN 201 CORRESPONDING TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 of MAN 202 CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE. MAN:203/204 (CHAIN C) CORRESPONDS TO MAN-ALPHA-1,2-MAN-ALPHA BOUND THROUGH THE LOW AFFINITY SITE WITH C1-C6 of MAN 203 CORRESPONDING TO THE REDUCING MANNOPYRANOSE RING AND C1-C6 of MAN 204 CORRESPONDING TO C1-C6 OF THE NONREDUCING PYRANOSE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
121CBCANH
131(H)CCH-COSY
141(H)CCH-TOCSY
15115N-SEPARATED HOHAHA
161QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
171DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM AND IN A LIQUID CRYSTALLINE MEDIUM (5% C12E5, R=0.96) (RUCKERT & OTTING (2000) J.AM.CHEM.SOC. 122, 7793-7797) MEASURED IN 2D IPAP (15N, 1H)-HSQC EXPERIMENTS (OTTIGER ET AL (1998) J.AM.CHEM.SOC. 131, 373-378)
181INTERMOLECULAR DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED/13C-SEPARATED AND 15N-SEPARATED NOE EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA
191INTRA-DISACCHARIDE AND INTER-MANNOPYRANOSE DISTANCE RESTRAINTS OBTAINED FROM 12C-FILTERED NOE AND HOHAHA EXPERIMENTS ON COMPLEXES COMPRISING 1:1 AND 1:2 CVN:MAN-ALPHA-(1,2)-MAN-ALPHA.
NMR detailsText: This structure is the restrained regularized mean structure. IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (with "atom" as the first column) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN ...Text: This structure is the restrained regularized mean structure. IN THIS ENTRY THE ELEVENTH COLUMN OF THE COORDINATES (with "atom" as the first column) REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE 50 INDIVIDUAL SIMULATED ANNEALING STRUCTURES HAVING ZERO DISTANCE VIOLATIONS GREATER THAN 0.2 A AND ZERO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEG. THE AVERAGE STRUCTURE WAS GENERATED BY BEST FITTING TO THE BACKBONE OF RESIDUES 1-101. NOTE THE OCCUPANCY FIELD in the tenth column has no meaning. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE HIGH AFFINITY SITE=0.36. AVE.RMS DIFF. TO MEAN FOR INTERFACIAL SIDE CHAINS AND DISACCHARIDE OF THE LOW AFFINITY SITE=0.58. RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, NOE, CDIH 6.389414E-03 0.717363 0.693234 8.897236E-03 9.181435E-02.

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Sample preparation

Sample conditionspH: 6.4 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002

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Processing

NMR softwareName: X-PLOR / Version: NIH / Developer: BRUNGER / Classification: refinement
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE OF THE 1:1 COMPLEX IN WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (BEWLEY AND CLORE ...Details: THE STRUCTURE OF THE 1:1 COMPLEX IN WHICH DISACCHARIDE IS BOUND EXCLUSIVELY THROUGH THE HIGH AFFINITY SITE WAS CALCULATED USING CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (BEWLEY AND CLORE (2000) J.AM.CHEM.SOC. 122, 6009-6016; WANG ET AL. (2001) EMBO. J., 19, 5635-5649 & REFS THEREIN) IN WHICH THE PROTEIN BACKBONE AND NON-INTERFACIAL SIDE CHAINS ARE HELD FIXED AND THE DISACCHARIDE AND INTERFACIAL SIDE CHAINS ARE FREE TO TRANSLATE AND ROTATE SUBJECT TO EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS. THE STRUCTURE OF THE DISACCHARIDE BOUND THROUGH THE LOW AFFINITY SITE IS A MODEL CALCULATED FROM A COMBINATION OF EXPERIMENTAL DISTANCE AND TORSION ANGLE RESTRAINTS, AND ADDITIONAL RESTRAINTS INTRODUCED ON THE BASIS OF SYMMETRY PRESENT BETWEEN THE TWO DOMAINS (HIGH AND LOW AFFINITY). THE NMR COORDINATES FOR MONOMERIC CVN (PDB ACC. 2EZM) WERE USED FOR THE STARTING COORDINATES WITH 2 EQ. OF MAN-ALPHA-1,2-MAN-ALPHA POSITIONED WITHIN 10 A OF THE PREVIOUSLY MAPPED CARBOHYDRATE BINDING SITES (BEWLEY & OTERO-QUINTERO (2001) J.AM.CHEM.SOC. IN PRESS).
NMR ensembleConformers calculated total number: 50 / Conformers submitted total number: 1

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