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- PDB-5dt1: Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-dir... -

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Basic information

Entry
Database: PDB / ID: 5dt1
TitleCrystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly neutralizing antibody
Components
  • Fab Heavy chain of broadly neutralizing antibody VRC26.25
  • Fab Light chain of broadly neutralizing antibody VRC26.25
KeywordsIMMUNE SYSTEM / VRC26 / CAP256 / V1V2 / HIV-1 / Env / Envelope / Broadly Neutralizing / superinfection
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsGorman, J. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2015
Title: New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency.
Authors: Doria-Rose, N.A. / Bhiman, J.N. / Roark, R.S. / Schramm, C.A. / Gorman, J. / Chuang, G.Y. / Pancera, M. / Cale, E.M. / Ernandes, M.J. / Louder, M.K. / Asokan, M. / Bailer, R.T. / Druz, A. / ...Authors: Doria-Rose, N.A. / Bhiman, J.N. / Roark, R.S. / Schramm, C.A. / Gorman, J. / Chuang, G.Y. / Pancera, M. / Cale, E.M. / Ernandes, M.J. / Louder, M.K. / Asokan, M. / Bailer, R.T. / Druz, A. / Fraschilla, I.R. / Garrett, N.J. / Jarosinski, M. / Lynch, R.M. / McKee, K. / O'Dell, S. / Pegu, A. / Schmidt, S.D. / Staupe, R.P. / Sutton, M.S. / Wang, K. / Wibmer, C.K. / Haynes, B.F. / Abdool-Karim, S. / Shapiro, L. / Kwong, P.D. / Moore, P.L. / Morris, L. / Mascola, J.R.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_special_symmetry / 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 / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _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 2.1Sep 27, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy chain of broadly neutralizing antibody VRC26.25
L: Fab Light chain of broadly neutralizing antibody VRC26.25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7233
Polymers51,1362
Non-polymers5871
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-17 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.016, 77.027, 85.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-356-

HOH

21L-564-

HOH

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Components

#1: Antibody Fab Heavy chain of broadly neutralizing antibody VRC26.25


Mass: 28083.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293 cells / Production host: Homo sapiens (human)
#2: Antibody Fab Light chain of broadly neutralizing antibody VRC26.25


Mass: 23052.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293 cells / Production host: Homo sapiens (human)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Crystals grown in a reservoir solution of 23% PEG 8000 and 0.1M HEPES pH 7.5 and flash frozen in liquid nitrogen with 20% PEG 400 as a cryoprotectant
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.954→42.614 Å / Num. obs: 33667 / % possible obs: 90.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 24.79 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Rrim(I) all: 0.125 / Χ2: 1.017 / Net I/av σ(I): 11.969 / Net I/σ(I): 10.2 / Num. measured all: 179032
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-2.041.60.32918410.8170.2830.4361.03950.4
2.04-2.121.90.30525670.8130.240.391.06270.8
2.12-2.222.50.30132260.8520.2120.3711.06187.8
2.22-2.343.50.31635740.8780.1890.3711.07597.9
2.34-2.4850.30436670.9390.1480.3391.06399.8
2.48-2.676.40.2737160.9610.1150.2941.052100
2.67-2.947.20.19536690.9840.0780.211.025100
2.94-3.377.40.13437160.990.0530.1441.065100
3.37-4.247.30.09237530.9940.0360.0990.943100
4.24-5070.07639380.9930.0310.0820.94299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OD1

4od1


Resolution: 1.954→42.614 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 1684 5.01 %
Rwork0.1693 31938 -
obs0.1716 33622 89.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.03 Å2 / Biso mean: 33.7624 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 1.954→42.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 72 333 3889
Biso mean--92.28 37.25 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073617
X-RAY DIFFRACTIONf_angle_d0.8894941
X-RAY DIFFRACTIONf_chiral_restr0.055561
X-RAY DIFFRACTIONf_plane_restr0.006626
X-RAY DIFFRACTIONf_dihedral_angle_d11.6072152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9537-2.01120.2542660.2451148121440
2.0112-2.07610.2845950.21831873196864
2.0761-2.15030.2671200.20732354247481
2.1503-2.23640.24541470.19762711285893
2.2364-2.33820.23661540.1782910306499
2.3382-2.46140.23161540.175829313085100
2.4614-2.61560.2251550.168829273082100
2.6156-2.81760.19861540.169229603114100
2.8176-3.1010.21751540.17429843138100
3.101-3.54960.19691590.159429713130100
3.5496-4.47130.18431590.143330213180100
4.4713-42.62360.21711670.16931483315100
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)
14.3091.1641-1.47411.2732-0.41781.293-0.0343-0.0607-0.0411-0.06980.0293-0.1122-0.06020.07330.01450.15620.0208-0.02220.1160.00270.107722.1988-21.3353-32.7523
24.155-1.0113-0.67013.3294-0.56417.1855-0.1862-0.3314-0.02630.35650.13230.1615-0.2752-0.00030.03640.19740.0066-0.03990.17380.00790.182-20.8442-13.833-23.775
33.0583-1.644-1.60833.21981.62883.46620.019-0.11590.06140.09760.0622-0.11740.04530.2426-0.06660.15-0.0299-0.03390.15790.01210.116616.9765-15.4095-11.6996
43.15643.17511.26915.75241.52072.75930.0053-0.0505-0.04420.03690.02740.05340.0787-0.0063-0.00230.09480.0486-0.01820.11690.00670.1534-12.5407-20.8981-11.8407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 114 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 115 through 214 )H0
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 107 )L0
4X-RAY DIFFRACTION4chain 'L' and (resid 108 through 210 )L0

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