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- PDB-3ma9: Crystal structure of gp41 derived protein complexed with fab 8066 -

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Basic information

Entry
Database: PDB / ID: 3ma9
TitleCrystal structure of gp41 derived protein complexed with fab 8066
Components
  • Fab8066 FAB ANTIBODY FRAGMENT, Heavy Chain
  • Fab8066 FAB ANTIBODY FRAGMENT, Light Chain
  • Transmembrane glycoprotein
KeywordsIMMUNE SYSTEM / GP41
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1860 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Transmembrane glycoprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, M. / Gustchina, E. / Louis, J. / Gustchina, A. / Wlodawer, A. / Clore, M.
CitationJournal: Plos Pathog. / Year: 2010
Title: Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41.
Authors: Gustchina, E. / Li, M. / Louis, J.M. / Anderson, D.E. / Lloyd, J. / Frisch, C. / Bewley, C.A. / Gustchina, A. / Wlodawer, A. / Clore, G.M.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_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.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane glycoprotein
H: Fab8066 FAB ANTIBODY FRAGMENT, Heavy Chain
L: Fab8066 FAB ANTIBODY FRAGMENT, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4715
Polymers73,4253
Non-polymers462
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-57 kcal/mol
Surface area28440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.527, 124.698, 133.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transmembrane glycoprotein / gp41


Mass: 24479.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW0
#2: Antibody Fab8066 FAB ANTIBODY FRAGMENT, Heavy Chain


Mass: 26305.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Antibody Fab8066 FAB ANTIBODY FRAGMENT, Light Chain


Mass: 22640.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2M dibasic Ammonium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: marccd 300 / Detector: CCD / Date: Apr 3, 2009 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 44497 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.099 / Net I/σ(I): 15.24
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.92 / Rsym value: 0.662 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CMR

2cmr


Resolution: 2.05→29.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.432 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24512 1414 3.2 %RANDOM
Rwork0.19257 ---
obs0.1943 43032 98.56 %-
all-44497 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20 Å2
2---2.41 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4781 0 2 442 5225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9446679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63525.628215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06215808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6491516
X-RAY DIFFRACTIONr_chiral_restr0.0850.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213699
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.82923087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.33234985
X-RAY DIFFRACTIONr_scbond_it6.89321817
X-RAY DIFFRACTIONr_scangle_it8.62131692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 97 -
Rwork0.288 2779 -
obs--87.6 %
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)
10.3123-0.0844-0.02911.6887-0.4570.8911-0.0015-0.06580.07160.1482-0.00840.07190.01110.06350.00990.02380.01310.00260.0773-0.00350.045617.547381.300873.055
20.14770.0586-0.12141.0630.79610.7911-0.05270.06840.03740.05970.0957-0.01610.0983-0.006-0.04310.06470.0067-0.02630.06980.0220.048621.597539.814353.7211
30.2720.372-0.1011.49580.5040.5561-0.06850.0490.033-0.16070.06080.1238-0.0413-0.12690.00760.0578-0.0024-0.05050.1260.05180.0955.902342.415745.6383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2H1 - 218
3X-RAY DIFFRACTION3L1 - 209

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