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- PDB-3rjq: Crystal structure of anti-HIV llama VHH antibody A12 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3rjq
TitleCrystal structure of anti-HIV llama VHH antibody A12 in complex with C186 gp120
Components
  • C186 gp120
  • Llama VHH A12
KeywordsViral Protein/Immune system / Ig VH domain / anti-HIV / Viral Protein-Immune system complex
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHuman immunodeficiency virus type 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsChen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. ...Chen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. / Verrips, T. / Mascola, J. / Kwong, P.D.
CitationJournal: To be Published
Title: Crystal structure of anti-HIV A12 VHH of llama antibody in complex with C1086 gp120
Authors: Chen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. / Verrips, T. / Mascola, J. / Kwong, P.D.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Structure summary
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C186 gp120
B: Llama VHH A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,98310
Polymers58,2132
Non-polymers1,7708
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint23 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.600, 66.600, 266.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein C186 gp120


Mass: 42324.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1
#2: Antibody Llama VHH A12


Mass: 15888.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM of KH2PO4, 24.2% PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.601→50 Å / Num. obs: 13406 / % possible obs: 68.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→23.473 Å / SU ML: 0.37 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2988 659 4.92 %
Rwork0.2551 --
all0.26 --
obs0.2572 13402 68.98 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.266 Å2 / ksol: 0.263 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--33.1835 Å2-0 Å2-0 Å2
2---33.1835 Å2-0 Å2
3----15.7071 Å2
Refinement stepCycle: LAST / Resolution: 2.601→23.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 112 0 3390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043470
X-RAY DIFFRACTIONf_angle_d0.8834698
X-RAY DIFFRACTIONf_dihedral_angle_d15.4611264
X-RAY DIFFRACTIONf_chiral_restr0.055529
X-RAY DIFFRACTIONf_plane_restr0.003593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.80140.5101220.3566380X-RAY DIFFRACTION11
2.8014-3.08270.3464870.34761490X-RAY DIFFRACTION42
3.0827-3.52750.36051800.31153335X-RAY DIFFRACTION91
3.5275-4.43940.27881790.25043675X-RAY DIFFRACTION99
4.4394-23.47350.27351910.22033863X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8374-0.6084-1.04080.58950.65334.02280.59770.6023-0.0512-0.4281-0.06590.1225-0.5574-2.2135-0.19540.41950.43830.1651.47890.35190.23153.024823.566-36.4179
20.52650.0462-0.79870.1602-0.3622.10620.32560.6774-0.07940.0265-0.18580.4323-0.133-2.6376-0.03240.18610.08760.16972.34190.05710.4104-13.39216.1432-20.0504
30.24890.0316-0.09610.2396-0.00590.29890.26840.18070.22350.21010.25060.02590.4038-0.40110.75720.0912-0.7114-0.05530.5295-0.101-0.068616.17127.2438-12.1085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 45:256 )A45 - 256
2X-RAY DIFFRACTION2( CHAIN A AND RESID 257:472 )A257 - 472
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:113 )B1 - 113

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